-
1
-
-
85027344824
-
-
Accessed 02 July 2011
-
ABINIT. (2010). http://www.abinit.org. Accessed 02 July 2011.
-
(2010)
-
-
-
3
-
-
0034375393
-
The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: Formulation and tests of the analytical derivatives
-
Amara, P., Field, M. J., Alhambra, C., & Gao, J. (2000). The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: Formulation and tests of the analytical derivatives. Theoretical Chemistry Accounts, 104, 336.
-
(2000)
Theoretical Chemistry Accounts
, vol.104
, pp. 336
-
-
Amara, P.1
Field, M.J.2
Alhambra, C.3
Gao, J.4
-
4
-
-
41249087856
-
General purpose molecular dynamics simulations fully implemented on graphics processing units
-
Anderson, J. A., Lorenz, C. D., & Travesset, A. (2008). General purpose molecular dynamics simulations fully implemented on graphics processing units. Journal of Computational Physics, 227, 5342.
-
(2008)
Journal of Computational Physics
, vol.227
, pp. 5342
-
-
Anderson, J.A.1
Lorenz, C.D.2
Travesset, A.3
-
5
-
-
4243810035
-
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
-
Aqvist, J., & Warshel, A. (1993). Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chemical Reviews, 93, 2523.
-
(1993)
Chemical Reviews
, vol.93
, pp. 2523
-
-
Aqvist, J.1
Warshel, A.2
-
6
-
-
43049102068
-
The SIESTA method; developments and applicability
-
Artacho, E., Anglada, E., Dieguez, O., Gale, J. D., Garcia, A., Junquera, J., Martin, R. M., Ordejon, P., Pruneda, J. M., Sanchez-Portal, D., & Soler, J. M. (2008). The SIESTA method; developments and applicability. Journal of Physics: Condensed Matter, 20, 064208.
-
(2008)
Journal of Physics: Condensed Matter
, vol.20
-
-
Artacho, E.1
Anglada, E.2
Dieguez, O.3
Gale, J.D.4
Garcia, A.5
Junquera, J.6
Martin, R.M.7
Ordejon, P.8
Pruneda, J.M.9
Sanchez-Portal, D.10
Soler, J.M.11
-
8
-
-
0030573150
-
Quantum chemical computations on parts of large molecules: The ab initio local self consistent field method
-
Assfeld, X., & Rivail, J. L. (1996). Quantum chemical computations on parts of large molecules: The ab initio local self consistent field method. Chemical Physics Letters, 263, 100.
-
(1996)
Chemical Physics Letters
, vol.263
, pp. 100
-
-
Assfeld, X.1
Rivail, J.L.2
-
9
-
-
0041853283
-
-
J. Gao & M. A. Thompson (Eds.), Washington: American Chemical Society
-
Assfeld, X., Ferre, N., & Rivail, J. L. (1998). In J. Gao & M. A. Thompson (Eds.), Combined quantum mechanical and molecular mechanical methods, ACS Symp. Ser. (Vol. 712, p. 234). Washington: American Chemical Society.
-
(1998)
Combined quantum mechanical and molecular mechanical methods, ACS Symp. Ser.
, vol.712
, pp. 234
-
-
Assfeld, X.1
Ferre, N.2
Rivail, J.L.3
-
10
-
-
0012050648
-
Quasiparticle calculations in solids
-
Aulbur, W. G., Jonsson, L., & Wilkins, J. W. (2000). Quasiparticle calculations in solids. Solid State Physics, 54, 1.
-
(2000)
Solid State Physics
, vol.54
, pp. 1
-
-
Aulbur, W.G.1
Jonsson, L.2
Wilkins, J.W.3
-
11
-
-
3743048569
-
Pseudopotentials that work: From H to Pu
-
Bachelet, G. B., Hamann, D. R., Schluter, M. (1982). Pseudopotentials that work: From H to Pu. Physical Review B, 26, 4199.
-
(1982)
Physical Review B
, vol.26
, pp. 4199
-
-
Bachelet, G.B.1
Hamann, D.R.2
Schluter, M.3
-
12
-
-
47549112084
-
Time-dependent and time-independent wavepacket approaches to reactive scattering and photodissociation dynamics
-
Balint-Kurti, G. G. (2008). Time-dependent and time-independent wavepacket approaches to reactive scattering and photodissociation dynamics. International Reviews in Physical Chemistry, 27, 507.
-
(2008)
International Reviews in Physical Chemistry
, vol.27
, pp. 507
-
-
Balint-Kurti, G.G.1
-
13
-
-
33749125733
-
Modified embedded-atom potentials for cubic materials and impurities
-
Baskes, M. I. (1992). Modified embedded-atom potentials for cubic materials and impurities. Physical Review B, 46, 2727.
-
(1992)
Physical Review B
, vol.46
, pp. 2727
-
-
Baskes, M.I.1
-
14
-
-
4243553426
-
Density-functional exchangeenergy approximation with correct asymptotic behavior
-
Becke, A. D. (1988). Density-functional exchangeenergy approximation with correct asymptotic behavior. Physical Review A, 38, 3098.
-
(1988)
Physical Review A
, vol.38
, pp. 3098
-
-
Becke, A.D.1
-
15
-
-
0000189651
-
Density-functional thermochemistry. III. The role of exact exchange
-
Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics, 98, 5648.
-
(1993)
Journal of Chemical Physics
, vol.98
, pp. 5648
-
-
Becke, A.D.1
-
16
-
-
67649101377
-
Generic coarse-grained model for protein folding and aggregation
-
Bereau, T., & Deserno, M. (2009). Generic coarse-grained model for protein folding and aggregation. Journal of Chemical Physics, 130, 235106.
-
(2009)
Journal of Chemical Physics
, vol.130
-
-
Bereau, T.1
Deserno, M.2
-
17
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Nola, A. D., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684.
-
(1984)
Journal of Chemical Physics
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Nola, A.D.4
Haak, J.R.5
-
18
-
-
65949084921
-
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
-
Betancourt, M. R., & Omovie, S. J. (2009). Pairwise energies for polypeptide coarse-grained models derived from atomic force fields. Journal of Chemical Physics, 130, 195103.
-
(2009)
Journal of Chemical Physics
, vol.130
-
-
Betancourt, M.R.1
Omovie, S.J.2
-
19
-
-
4344626411
-
-
Theoretical Biophysics Group, University of Illinois and Beckman Institute, Accessed 02 July 2011
-
Bhandarkar, M., Bhatele, A., Bohm, E., Brunner, R., Buelens, F., Chipot, C., Dalke, A., Dixit, S., Fiorin, G., Freddolino, P., Grayson, P., Gullingsrud, J., Gursoy, A., Hardy, D., Harrison, C., Henin, J., Humphrey, W., Hurwitz, D., Krawetz, N., Kumar, S., Kunzman, D., Lee, C., Mei, C., Nelson, M., Phillips, J., Sarood, O., Shinozaki, A., Zheng, G., & Zhu, F. (2009). NAMD User’s Guide. Theoretical Biophysics Group, University of Illinois and Beckman Institute. http://www.ks.uiuc.edu/Research/namd/. Accessed 02 July 2011.
-
(2009)
NAMD User’s Guide
-
-
Bhandarkar, M.1
Bhatele, A.2
Bohm, E.3
Brunner, R.4
Buelens, F.5
Chipot, C.6
Dalke, A.7
Dixit, S.8
Fiorin, G.9
Freddolino, P.10
Grayson, P.11
Gullingsrud, J.12
Gursoy, A.13
Hardy, D.14
Harrison, C.15
Henin, J.16
Humphrey, W.17
Hurwitz, D.18
Krawetz, N.19
Kumar, S.20
Kunzman, D.21
Lee, C.22
Mei, C.23
Nelson, M.24
Phillips, J.25
Sarood, O.26
Shinozaki, A.27
Zheng, G.28
Zhu, F.29
more..
-
20
-
-
25744460922
-
Projector augmented-wave method
-
Blochl, P. E. (1994). Projector augmented-wave method. Physical Review B, 50, 17953.
-
(1994)
Physical Review B
, vol.50
, pp. 17953
-
-
Blochl, P.E.1
-
21
-
-
0037288369
-
Projector augmented wave method: Ab initiomolecular dynamics with full wave functions
-
Blochl, P. E., Forst, C. J., & Schimpl, J. (2003). Projector augmented wave method: Ab initiomolecular dynamics with full wave functions. Bulletin of Material Science, 26, 33.
-
(2003)
Bulletin of Material Science
, vol.26
, pp. 33
-
-
Blochl, P.E.1
Forst, C.J.2
Schimpl, J.3
-
22
-
-
0031362068
-
Density-functional theory calculations for poly-atomic systems: Electronic structure, static and elastic properties and ab initio molecular dynamics
-
Bockstedte, M., Kley, A., Neugebauer, J., & Scheffler, M. (1997). Density-functional theory calculations for poly-atomic systems: Electronic structure, static and elastic properties and ab initio molecular dynamics. Computer Physics Communications, 107, 187.
-
(1997)
Computer Physics Communications
, vol.107
, pp. 187
-
-
Bockstedte, M.1
Kley, A.2
Neugebauer, J.3
Scheffler, M.4
-
24
-
-
33646139389
-
Recent progress with largescale ab initio calculations: The CONQUEST code
-
Bowler, D. R., Choudhury, R., Gillan, M. J., & Miyazaki, T. (2006). Recent progress with largescale ab initio calculations: The CONQUEST code. Physica Status Solidi B, 243, 989.
-
(2006)
Physica Status Solidi B
, vol.243
, pp. 989
-
-
Bowler, D.R.1
Choudhury, R.2
Gillan, M.J.3
Miyazaki, T.4
-
25
-
-
84890021933
-
The calculation of small molecular interactions by the differences of separate total energies. some procedures with reduced errors
-
Boys, S. F., & Bernardi, F. (1970). The calculation of small molecular interactions by the differences of separate total energies. some procedures with reduced errors. Molecular Physics, 19, 553.
-
(1970)
Molecular Physics
, vol.19
, pp. 553
-
-
Boys, S.F.1
Bernardi, F.2
-
26
-
-
84962440885
-
Theory and range of modern semiempirical molecular orbital methods
-
Bredow, T., & Jug, K. (2005). Theory and range of modern semiempirical molecular orbital methods. Theoretical Chemistry Accounts, 113, 1.
-
(2005)
Theoretical Chemistry Accounts
, vol.113
, pp. 1
-
-
Bredow, T.1
Jug, K.2
-
27
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B. R., Brooks, C. L., III, Mackerell, A.D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M.,&Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30, 1545.
-
(2009)
Journal of Computational Chemistry
, vol.30
, pp. 1545
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
28
-
-
0001546949
-
The classical equation of state of gaseous helium, neon and argon
-
Buckingham, R. A. (1938). The classical equation of state of gaseous helium, neon and argon. Proceedings of the Royal Society of London A, 168, 264.
-
(1938)
Proceedings of the Royal Society of London A
, vol.168
, pp. 264
-
-
Buckingham, R.A.1
-
29
-
-
73349125800
-
Toward a practical method for adaptive QM/MM simulations
-
Bulo, R. E., Ensing, B., Sikkema, J., & Visscher, L. (2009). Toward a practical method for adaptive QM/MM simulations. Journal of Chemical Theory and Computation, 5, 2212.
-
(2009)
Journal of Chemical Theory and Computation
, vol.5
, pp. 2212
-
-
Bulo, R.E.1
Ensing, B.2
Sikkema, J.3
Visscher, L.4
-
30
-
-
4243606192
-
Unified approach for molecular dynamics and density-functional theory
-
Car, R., & Parrinello, M. (1985). Unified approach for molecular dynamics and density-functional theory. Physical Review Letters, 55, 2471.
-
(1985)
Physical Review Letters
, vol.55
, pp. 2471
-
-
Car, R.1
Parrinello, M.2
-
31
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Jr., K. M. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1668
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Onufriev, A.6
Simmerling, C.7
Wang, B.8
Woods, R.9
-
32
-
-
58049201323
-
-
San Francisco: University of California, Accessed 02 July 2011
-
Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowley, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., KolossvA!ry, I., Wong, F. K., Paesani, F., Vanicek, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., & Kollman, P. (2008). AMBER 10. San Francisco: University of California. http:// ambermd.org/. Accessed 02 July 2011.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossv Ary, I.16
Wong, F.K.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.33
more..
-
33
-
-
85027346192
-
-
Accessed 02 July 2011
-
CASTEP. (2009). http://www.tcm.phy.cam.ac.uk/castep/. Accessed 02 July 2011.
-
(2009)
-
-
-
35
-
-
12344328934
-
Special points in the brillouin zone
-
Chadi, D. J., & Cohen, M. L. (1973). Special points in the brillouin zone. Physical Review B, 8, 5747.
-
(1973)
Physical Review B
, vol.8
, pp. 5747
-
-
Chadi, D.J.1
Cohen, M.L.2
-
36
-
-
85027370192
-
-
Accessed 02 July 2011
-
CHARMM. (2009). http://www.charmm.org/. Accessed 02 July 2011.
-
(2009)
-
-
-
37
-
-
20144380685
-
First principles methods using CASTEP
-
Clark, S. J., Segall, M. D., Pickard, C. J., Hasnip, P. J., Probert, M. J., Refson, K., & Payne, M. C. (2005). First principles methods using CASTEP. Zeitschrift fur Kristallographie, 220, 567.
-
(2005)
Zeitschrift fur Kristallographie
, vol.220
, pp. 567
-
-
Clark, S.J.1
Segall, M.D.2
Pickard, C.J.3
Hasnip, P.J.4
Probert, M.J.5
Refson, K.6
Payne, M.C.7
-
38
-
-
85027330070
-
-
Accessed 02 July 2011
-
CONQUEST. (2009). http://hamlin.phys.ucl.ac.uk/NewCQWeb/bin/view. Accessed 02 July 2011.
-
(2009)
-
-
-
39
-
-
27244452976
-
Tunable generic model for fluid bilayer membranes
-
Cooke, I. R., Kremer, K., & Deserno, M. (2005). Tunable generic model for fluid bilayer membranes. Physical Review E, 72, 011506.
-
(2005)
Physical Review E
, vol.72
-
-
Cooke, I.R.1
Kremer, K.2
Deserno, M.3
-
40
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of American Chemical Society, 117, 5179.
-
(1995)
Journal of American Chemical Society
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
41
-
-
85027306809
-
-
Accessed 02 July 2011
-
CP-PAW. (2006). http://orion.pt.tu-clausthal.de/paw/. Accessed 02 July 2011.
-
(2006)
-
-
-
42
-
-
0002077637
-
Geometry optimization by direct inversion in the iterative subspace
-
Csaszar, P., & Pulay, P. (1984). Geometry optimization by direct inversion in the iterative subspace. Journal of Molecular Structure, 114, 31.
-
(1984)
Journal of Molecular Structure
, vol.114
, pp. 31
-
-
Csaszar, P.1
Pulay, P.2
-
43
-
-
85027295074
-
-
Accessed 02 July 2011
-
DACAPO. (2006). https://wiki.fysik.dtu.dk/dacapo. Accessed 02 July 2011.
-
(2006)
-
-
-
44
-
-
4244024430
-
Semiempirical, quantum mechanical calculation of hydrogen embrittlement in metals
-
Daw, M. S., & Baskes, M. I. (1983). Semiempirical, quantum mechanical calculation of hydrogen embrittlement in metals. Physical Review Letters, 50, 1285.
-
(1983)
Physical Review Letters
, vol.50
, pp. 1285
-
-
Daw, M.S.1
Baskes, M.I.2
-
45
-
-
4244079381
-
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
-
Daw, M. S., & Baskes, M. I. (1984). Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals. Physical Review B, 29, 6443.
-
(1984)
Physical Review B
, vol.29
, pp. 6443
-
-
Daw, M.S.1
Baskes, M.I.2
-
46
-
-
0000138517
-
An effective fragment method for modeling solvent effects in quantum mechanical calculations
-
Day, P. N., Jensen, J. H., Gordon, M. S., Webb, S. P., Stevens, W. J., Krauss, M., Garmer, D., Basch, H., & Cohen, D. (1996). An effective fragment method for modeling solvent effects in quantum mechanical calculations. Journal of Chemical Physics, 105, 1968.
-
(1996)
Journal of Chemical Physics
, vol.105
, pp. 1968
-
-
Day, P.N.1
Jensen, J.H.2
Gordon, M.S.3
Webb, S.P.4
Stevens, W.J.5
Krauss, M.6
Garmer, D.7
Basch, H.8
Cohen, D.9
-
48
-
-
85027333669
-
-
J. Grotendorst, S. Blugel, & D. Marx (Eds.), Julich: NIC, Accessed 02 July 2011
-
Doltsinis, N. L. (2006). In J. Grotendorst, S. Blugel, & D. Marx (Eds.), Computational nanoscience: Do it yourself! Julich: NIC. http://www2. fz-juelich.de/nic- series/volume31/doltsinis3. pdf. Accessed 02 July 2011.
-
(2006)
Computational nanoscience: Do it yourself!
-
-
Doltsinis, N.L.1
-
49
-
-
0037156912
-
Nonadiabatic car-parrinello molecular dynamics
-
Doltsinis, N. L., & Marx, D. (2002a). Nonadiabatic car-parrinello molecular dynamics. Physical Review Letters, 88, 166402.
-
(2002)
Physical Review Letters
, vol.88
-
-
Doltsinis, N.L.1
Marx, D.2
-
50
-
-
0012987210
-
First-principles molecular dynamics involving excited states and nonadiabatic transitions
-
Doltsinis, N. L., & Marx, D. (2002b). First-principles molecular dynamics involving excited states and nonadiabatic transitions. Journal of Theoretical and Computational Chemistry, 1, 319-349.
-
(2002)
Journal of Theoretical and Computational Chemistry
, vol.1
, pp. 319-349
-
-
Doltsinis, N.L.1
Marx, D.2
-
52
-
-
33745948989
-
A systematic method to derive force fields for coarse-grained simulations of phospholipids
-
Elezgaray, J., & Laguerre, M. (2006). A systematic method to derive force fields for coarse-grained simulations of phospholipids. Computer Physics Communications, 175, 264.
-
(2006)
Computer Physics Communications
, vol.175
, pp. 264
-
-
Elezgaray, J.1
Laguerre, M.2
-
53
-
-
1542779956
-
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
-
Elstner, M., Porezag, D., Jungnickel, G., Elsner, J., Haugk, M., Frauenheim, T., Suhai, S., & Seifert, G. (1998). Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Physical Review B, 58, 7260.
-
(1998)
Physical Review B
, vol.58
, pp. 7260
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seifert, G.8
-
54
-
-
84977266737
-
Die Berechnung optischer und elektrostatischer Gitterpotentiale
-
Ewald, P. P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annals of Physics, 369, 253.
-
(1921)
Annals of Physics
, vol.369
, pp. 253
-
-
Ewald, P.P.1
-
55
-
-
0037197652
-
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method
-
Ferre, N., Assfeld, X., & Rivail, J. L. (2002). Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method. Journal of Computational Chemistry, 23, 610.
-
(2002)
Journal of Computational Chemistry
, vol.23
, pp. 610
-
-
Ferre, N.1
Assfeld, X.2
Rivail, J.L.3
-
56
-
-
85027337379
-
-
Accessed 02 July 2011
-
FHI98md. (2002). http://www.fhi-berlin.mpg.de/th/fhimd/. Accessed 02 July 2011.
-
(2002)
-
-
-
57
-
-
16344375443
-
A simple empirical n-body potential for transition metals
-
Finnis, M. W., & Sinclair, J. E. (1984). A simple empirical n-body potential for transition metals. Philosophical Magazine A, 29, 6443.
-
(1984)
Philosophical Magazine A
, vol.29
, pp. 6443
-
-
Finnis, M.W.1
Sinclair, J.E.2
-
58
-
-
0242474475
-
Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding
-
Fornili, A., Sironi, M., & Raimondi, M. (2003). Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding. Journal of Molecular Structure (THEOCHEM), 632, 157.
-
(2003)
Journal of Molecular Structure (THEOCHEM)
, vol.632
, pp. 157
-
-
Fornili, A.1
Sironi, M.2
Raimondi, M.3
-
59
-
-
33746363887
-
Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods
-
Fornili, A., Loos, P.-F., Sironi, M., & Assfeld, X. (2006a). Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods. Chemical Physics Letters, 427, 236.
-
(2006)
Chemical Physics Letters
, vol.427
, pp. 236
-
-
Fornili, A.1
Loos, P.-F.2
Sironi, M.3
Assfeld, X.4
-
60
-
-
33644887128
-
On the suitability of strictly localized orbitals for hybrid QM/MM calculations
-
Fornili, A., Moreau, Y., Sironi, M., & Assfeld, X. (2006b). On the suitability of strictly localized orbitals for hybrid QM/MM calculations. Journal of Computational Chemistry, 27, 515.
-
(2006)
Journal of Computational Chemistry
, vol.27
, pp. 515
-
-
Fornili, A.1
Moreau, Y.2
Sironi, M.3
Assfeld, X.4
-
61
-
-
85027314124
-
-
Accessed 02 July 2011
-
Free Molecular Visualization Software. (2008). http://www.umass.edu/microbio/rasmol/othersof. htm. Accessed 02 July 2011.
-
(2008)
-
-
-
62
-
-
2742548473
-
Ionic sizes and born repulsive parameters in the NaCl-type alkali halides I: The Huggins-Mayer and Pauling forms
-
Fumi, F. G., & Tosi, M. P. (1964). Ionic sizes and born repulsive parameters in the NaCl-type alkali halides I: The Huggins-Mayer and Pauling forms. Journal of Physics and Chemitry of Solids, 25, 31.
-
(1964)
Journal of Physics and Chemitry of Solids
, vol.25
, pp. 31
-
-
Fumi, F.G.1
Tosi, M.P.2
-
63
-
-
0000411659
-
A Generalized Hybrid Orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations
-
Gao, J., Amara, P., Alhambra, C., & Field, M. J. (1998). A Generalized Hybrid Orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations. Journal of Physics Chemistry A, 102, 4714.
-
(1998)
Journal of Physics Chemistry A
, vol.102
, pp. 4714
-
-
Gao, J.1
Amara, P.2
Alhambra, C.3
Field, M.J.4
-
64
-
-
2442538904
-
Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method
-
Garcia-Viloca, M., & Gao, J. (2004). Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method. Theoretical Chemistry Accounts, 111, 280.
-
(2004)
Theoretical Chemistry Accounts
, vol.111
, pp. 280
-
-
Garcia-Viloca, M.1
Gao, J.2
-
65
-
-
70349568754
-
QUANTUM ESPRESSO: A modular and open-source software project for quantum simulations of materials
-
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococcioni, M., Dabo, I., Corso, A. D., Fabris, S., Fratesi, G., de Gironcoli, S., Gebauer, R., Gerstmann, U., Gougoussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Scandolo, S., Sclauzero, G., Seitsonen, A. P., Smogunov, A., Umari, P., & Wentzcovitch, R. M. (2009). QUANTUM ESPRESSO: A modular and open-source software project for quantum simulations of materials. Journal of Physics: Condensed Matter, 21, 395502.
-
(2009)
Journal of Physics: Condensed Matter
, vol.21
-
-
Giannozzi, P.1
Baroni, S.2
Bonini, N.3
Calandra, M.4
Car, R.5
Cavazzoni, C.6
Ceresoli, D.7
Chiarotti, G.L.8
Cococcioni, M.9
Dabo, I.10
Corso, A.D.11
Fabris, S.12
Fratesi, G.13
De Gironcoli, S.14
Gebauer, R.15
Gerstmann, U.16
Gougoussis, C.17
Kokalj, A.18
Lazzeri, M.19
Martin-Samos, L.20
Marzari, N.21
Mauri, F.22
Mazzarello, R.23
Paolini, S.24
Pasquarello, A.25
Paulatto, L.26
Sbraccia, C.27
Scandolo, S.28
Sclauzero, G.29
Seitsonen, A.P.30
Smogunov, A.31
Umari, P.32
Wentzcovitch, R.M.33
more..
-
66
-
-
0000160164
-
Separable dual-space Gaussian pseudopotentials
-
Goedecker, S., Teter, M., & Hutter, J. (1996). Separable dual-space Gaussian pseudopotentials. Physical Review B, 54, 1703.
-
(1996)
Physical Review B
, vol.54
, pp. 1703
-
-
Goedecker, S.1
Teter, M.2
Hutter, J.3
-
67
-
-
0000283071
-
Mobility and elasticity of self-assembled membranes
-
Goetz, R., Compper, G., & Lipowsky, R. (1999). Mobility and elasticity of self-assembled membranes. Physical Review Letters, 82, 221.
-
(1999)
Physical Review Letters
, vol.82
, pp. 221
-
-
Goetz, R.1
Compper, G.2
Lipowsky, R.3
-
68
-
-
0035138053
-
The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry
-
Gordon, M. S., Freitag, M. A., Bandyopadhyay, P., Jensen, J. H., Kairys, V., & Stevens, W. J. (2001). The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry. The Journal of Physical Chemistry A, 105, 105.
-
(2001)
The Journal of Physical Chemistry A
, vol.105
, pp. 105
-
-
Gordon, M.S.1
Freitag, M.A.2
Bandyopadhyay, P.3
Jensen, J.H.4
Kairys, V.5
Stevens, W.J.6
-
69
-
-
0037038563
-
Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments
-
Grigorenko, B. L., Nemukhin, A. V., Topol, I. A., & Burt, S. K. (2002). Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments. The Journal of Physical Chemistry A, 106, 10663.
-
(2002)
The Journal of Physical Chemistry A
, vol.106
, pp. 10663
-
-
Grigorenko, B.L.1
Nemukhin, A.V.2
Topol, I.A.3
Burt, S.K.4
-
71
-
-
24544460330
-
Norm-conserving pseudopotentials
-
Hamann, D. R., Schluter, M., Chiang, C. (1979). Norm-conserving pseudopotentials. Physical Review Letters, 43, 1494.
-
(1979)
Physical Review Letters
, vol.43
, pp. 1494
-
-
Hamann, D.R.1
Schluter, M.2
Chiang, C.3
-
72
-
-
0000083717
-
Relativistic separable dual-space Gaussian pseudopotentials from H to Rn
-
Hartwigsen, C., Goedecker, S., & Hutter, J. (1998). Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. Physical Review B, 58, 3641.
-
(1998)
Physical Review B
, vol.58
, pp. 3641
-
-
Hartwigsen, C.1
Goedecker, S.2
Hutter, J.3
-
73
-
-
33947392043
-
Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations
-
Heyden, A., Lin, H., & Truhlar, D.G. (2007). Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. The Journal of Physical Chemistry B, 111, 2231.
-
(2007)
The Journal of Physical Chemistry B
, vol.111
, pp. 2231
-
-
Heyden, A.1
Lin, H.2
Truhlar, D.G.3
-
74
-
-
0000432120
-
The potential calculation and some applications
-
Hockney, R. W. (1970). The potential calculation and some applications. Methods in Computational Physics, 9, 135.
-
(1970)
Methods in Computational Physics
, vol.9
, pp. 135
-
-
Hockney, R.W.1
-
76
-
-
26844440098
-
Structure and dynamics of solvated Sn(II) in aqueous solution: An ab initio QM/MM MD approach
-
Hofer, T. S., Pribil, A. B., Randolf, B. R.,&Rode, B. M. (2005). Structure and dynamics of solvated Sn(II) in aqueous solution: An ab initio QM/MM MD approach. Journal of American Chemical Society, 127, 14231.
-
(2005)
Journal of American Chemical Society
, vol.127
, pp. 14231
-
-
Hofer, T.S.1
Pribil, A.B.2
Randolf, B.R.3
Rode, B.M.4
-
77
-
-
85027298170
-
-
Accessed 02 July 2011
-
HOOMD. (2009). http://codeblue.umich.edu/hoomdblue. Accessed 02 July 2011.
-
(2009)
-
-
-
78
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31, 1695.
-
(1985)
Physical Review A
, vol.31
, pp. 1695
-
-
Hoover, W.G.1
-
79
-
-
33646645973
-
Constant-pressure equations of motion
-
Hoover, W. G. (1986). Constant-pressure equations of motion. Physical Review A, 34, 2499.
-
(1986)
Physical Review A
, vol.34
, pp. 2499
-
-
Hoover, W.G.1
-
80
-
-
0028392759
-
Electronic structure optimization in planewave-based density functional calculations by direct inversion in the iterative subspace
-
Hutter, J., Luthi, H. P., & Parrinello, M. (1994). Electronic structure optimization in planewave-based density functional calculations by direct inversion in the iterative subspace. Computational Materials Science, 2, 244.
-
(1994)
Computational Materials Science
, vol.2
, pp. 244
-
-
Hutter, J.1
Luthi, H.P.2
Parrinello, M.3
-
81
-
-
85027359928
-
-
Accessed 02 July 2011
-
Hutter, J., Kohlmeyer, A., Mundy, C. J., Mohamed, F., Schiffmann, F., Tabacchi, G., Forbert, H., Bethune, I., Kuo, W., Krack, M., Iannuzzi, M., Guidon, M., McGrath, M., Kuehne, T. D., Laino, T., Borstnik, U., VandeVondele, J., & Weber, V. (2009). CP2K - a general program to perform molecular dynamics simulations. http://cp2k.berlios.de. Accessed 02 July 2011.
-
(2009)
CP2K - a general program to perform molecular dynamics simulations
-
-
Hutter, J.1
Kohlmeyer, A.2
Mundy, C.J.3
Mohamed, F.4
Schiffmann, F.5
Tabacchi, G.6
Forbert, H.7
Bethune, I.8
Kuo, W.9
Krack, M.10
Iannuzzi, M.11
Guidon, M.12
McGrath, M.13
Kuehne, T.D.14
Laino, T.15
Borstnik, U.16
VandeVondele, J.17
Weber, V.18
-
82
-
-
34247852737
-
-
Accessed 02 July 2011
-
ICSD. (2009). Inorganic crystal structure database. http://www.fiz-karlsruhe.de/icsd.html. Accessed 02 July 2011.
-
(2009)
Inorganic crystal structure database
-
-
-
83
-
-
14544291957
-
Amultiscale coarsegraining method for biomolecular systems
-
Izvekov, S., & Voth, G. A. (2005). Amultiscale coarsegraining method for biomolecular systems. The Journal of Physical Chemistry B, 109, 2469.
-
(2005)
The Journal of Physical Chemistry B
, vol.109
, pp. 2469
-
-
Izvekov, S.1
Voth, G.A.2
-
84
-
-
33748250745
-
Multiscale coarsegraining of mixed phospholipid/cholesterol bilayers
-
Izvekov, S., & Voth, G. A. (2006). Multiscale coarsegraining of mixed phospholipid/cholesterol bilayers. Journal of Chemical Theory and Computation, 2, 637.
-
(2006)
Journal of Chemical Theory and Computation
, vol.2
, pp. 637
-
-
Izvekov, S.1
Voth, G.A.2
-
86
-
-
0038391194
-
-
D. A. Smith (Ed.), Washington, DC: American Chemical Society
-
Jensen, J. H., Day, P. N., Gordon, M. S., Basch, H., Cohen, D., Garmer, D. R., Krauss, M., & Stevens, W. J. (1994). In D. A. Smith (Ed.), Modeling the hydrogen bond, ACS Symp. Ser. (Vol. 569, p. 139). Washington, DC: American Chemical Society.
-
(1994)
Modeling the hydrogen bond, ACS Symp. Ser.
, vol.569
, pp. 139
-
-
Jensen, J.H.1
Day, P.N.2
Gordon, M.S.3
Basch, H.4
Cohen, D.5
Garmer, D.R.6
Krauss, M.7
Stevens, W.J.8
-
87
-
-
0021515659
-
Optimized intermolecular potential functions for liquid hydrocarbons
-
Jorgensen, W. L., Madura, J. D., & Swenson, C. J. (1984). Optimized intermolecular potential functions for liquid hydrocarbons. Journal of American Chemical Society, 106, 6638.
-
(1984)
Journal of American Chemical Society
, vol.106
, pp. 6638
-
-
Jorgensen, W.L.1
Madura, J.D.2
Swenson, C.J.3
-
88
-
-
36348953683
-
New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
-
Jung, J., Choi, C. H., Sugita, Y., & Ten-no, S. (2007). New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals. Journal of Chemical Physics, 127, 204102.
-
(2007)
Journal of Chemical Physics
, vol.127
-
-
Jung, J.1
Choi, C.H.2
Sugita, Y.3
Tenno, S.4
-
89
-
-
0034225741
-
QM/MM boundaries across covalent bonds: A frozen localized molecular orbital-based approach for the effective fragment potential method
-
Kairys, V., & Jensen, J. H. (2000). QM/MM boundaries across covalent bonds: A frozen localized molecular orbital-based approach for the effective fragment potential method. The Journal of Physical Chemistry A, 104, 6656.
-
(2000)
The Journal of Physical Chemistry A
, vol.104
, pp. 6656
-
-
Kairys, V.1
Jensen, J.H.2
-
90
-
-
53849111603
-
Generalized Langevin equation for solids. I. Rigorous derivation and main properties
-
Kantorovich, L. (2008). Generalized Langevin equation for solids. I. Rigorous derivation and main properties. Physical Review B, 78, 094304.
-
(2008)
Physical Review B
, vol.78
-
-
Kantorovich, L.1
-
91
-
-
53849103637
-
Generalized Langevin equation for solids. II. Stochastic boundary conditions for nonequilibrium molecular dynamics simulations
-
Kantorovich, L., & Rompotis, N. (2008). Generalized Langevin equation for solids. II. Stochastic boundary conditions for nonequilibrium molecular dynamics simulations. Physical Review B, 78, 094305.
-
(2008)
Physical Review B
, vol.78
-
-
Kantorovich, L.1
Rompotis, N.2
-
92
-
-
0034625269
-
High performance computational chemistry: An overview of NWChem a distributed parallel application
-
Kendall, R. A., Apra, E., Bernholdt, D. E., Bylaska, E. J., Dupuis, M., Fann, G. I., Harrison, R. J., Ju, J., Nichols, J. A., Nieplocha, J., Straatsma, T. P., Windus, T. L., & Wong, A. T. (2000). High performance computational chemistry: An overview of NWChem a distributed parallel application. Computer Physics Communications, 128, 260.
-
(2000)
Computer Physics Communications
, vol.128
, pp. 260
-
-
Kendall, R.A.1
Apra, E.2
Bernholdt, D.E.3
Bylaska, E.J.4
Dupuis, M.5
Fann, G.I.6
Harrison, R.J.7
Ju, J.8
Nichols, J.A.9
Nieplocha, J.10
Straatsma, T.P.11
Windus, T.L.12
Wong, A.T.13
-
94
-
-
0009662619
-
ONIOMXS: An extension of the ONIOM method for molecular simulation in condensed phase
-
Kerdcharoen, T., & Morokuma, K. (2002). ONIOMXS: An extension of the ONIOM method for molecular simulation in condensed phase. Chemical Physics Letters, 355, 257.
-
(2002)
Chemical Physics Letters
, vol.355
, pp. 257
-
-
Kerdcharoen, T.1
Morokuma, K.2
-
95
-
-
3743131895
-
Non-singular atomic pseudopotentials for solid state applications
-
Kerker, G. (1980). Non-singular atomic pseudopotentials for solid state applications. The Journal of Physical Chemistry C, 13, L189.
-
(1980)
The Journal of Physical Chemistry C
, vol.13
, pp. L189
-
-
Kerker, G.1
-
96
-
-
58749084517
-
DNA and lipid bilayers: Self-assembly and insertion
-
Khalid, S., Bond, P. J., Holyoake, J., Hawtin, R. W., & Sansom, M. S. P. (2008). DNA and lipid bilayers: Self-assembly and insertion. Journal of the Royal Society Interface, 5, S241.
-
(2008)
Journal of the Royal Society Interface
, vol.5
, pp. S241
-
-
Khalid, S.1
Bond, P.J.2
Holyoake, J.3
Hawtin, R.W.4
Sansom, M.S.P.5
-
98
-
-
77956715009
-
Adiabatic approximation and its accuracy
-
Kołos, W. (1970). Adiabatic approximation and its accuracy. Advances in Quantum Chemistry, 5, 99.
-
(1970)
Advances in Quantum Chemistry
, vol.5
, pp. 99
-
-
Kołos, W.1
-
99
-
-
0343417367
-
Dynamics of entangled linear polymer melts: A moleculardynamics simulation
-
Kremer, K., & Grest, G. (1990). Dynamics of entangled linear polymer melts: A moleculardynamics simulation. Journal of Chemical Physics, 92, 5057.
-
(1990)
Journal of Chemical Physics
, vol.92
, pp. 5057
-
-
Kremer, K.1
Grest, G.2
-
100
-
-
2442537377
-
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
-
Kresse, G., & Furthmuller, J. (1996). Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Physical Review B, 54, 11169.
-
(1996)
Physical Review B
, vol.54
, pp. 11169
-
-
Kresse, G.1
Furthmuller, J.2
-
101
-
-
4444372137
-
Liquid water from first principles: Investigation of different sampling approaches
-
Kuo, I.-F. W., Mundy, C. J., McGrath, M. J., Siepmann, J. I., VandeVondele, J., Sprik, M., Hutter, J., Chen, B., Klein, M. L., Mohamed, F., Krack, M., & Parrinello, M. (2004). Liquid water from first principles: Investigation of different sampling approaches. The Journal of Physical Chemistry B, 108, 12990.
-
(2004)
The Journal of Physical Chemistry B
, vol.108
, pp. 12990
-
-
Kuo, I.-F.W.1
Mundy, C.J.2
McGrath, M.J.3
Siepmann, J.I.4
VandeVondele, J.5
Sprik, M.6
Hutter, J.7
Chen, B.8
Klein, M.L.9
Mohamed, F.10
Krack, M.11
Parrinello, M.12
-
102
-
-
0001242174
-
The adiabatic approximation I. The physical background of the Born-Handy ansatz
-
Kutzelnigg, W. (1997). The adiabatic approximation I. The physical background of the Born-Handy ansatz. Molecular Physics, 90, 909.
-
(1997)
Molecular Physics
, vol.90
, pp. 909
-
-
Kutzelnigg, W.1
-
103
-
-
34247648401
-
Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials
-
Laasonen, K., Pasquarello, A., Car, R., Lee, C., & Vanderbilt, D. (1993). Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials. Physical Review B, 47, 10142.
-
(1993)
Physical Review B
, vol.47
, pp. 10142
-
-
Laasonen, K.1
Pasquarello, A.2
Car, R.3
Lee, C.4
Vanderbilt, D.5
-
104
-
-
0037156101
-
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
-
Laio, A., VandeVondele, J.,&Rothlisberger, U. (2002). A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. Journal of Chemical Physics, 116, 6941.
-
(2002)
Journal of Chemical Physics
, vol.116
, pp. 6941
-
-
Laio, A.1
VandeVondele, J.2
Rothlisberger, U.3
-
105
-
-
85027316359
-
-
Accessed 02 July 2011
-
LAMMPS. (2010). http://lammps.sandia.gov/. Accessed 02 July 2011.
-
(2010)
-
-
-
106
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee, C., Yang, W., & Parr, R. C. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785.
-
(1988)
Physical Review B
, vol.37
, pp. 785
-
-
Lee, C.1
Yang, W.2
Parr, R.C.3
-
107
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E., Hess, B., & van der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7, 306.
-
(2001)
Journal of Molecular Modeling
, vol.7
, pp. 306
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
109
-
-
0002997010
-
A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems
-
Luty, B. A., Davis, M. E., Tironi, I. G., & van Gunsteren, W. F. (1994). A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems. Molecular Simulation, 14, 11.
-
(1994)
Molecular Simulation
, vol.14
, pp. 11
-
-
Luty, B.A.1
Davis, M.E.2
Tironi, I.G.3
Van Gunsteren, W.F.4
-
110
-
-
0000642278
-
Lattice-summethods for calculating electrostatic interactions in molecular simulations
-
Luty, B. A., Tironi, I. G., & van Gunsteren, W. F. (1995). Lattice-summethods for calculating electrostatic interactions in molecular simulations. Journal of Chemical Physics, 103, 3014.
-
(1995)
Journal of Chemical Physics
, vol.103
, pp. 3014
-
-
Luty, B.A.1
Tironi, I.G.2
Van Gunsteren, W.F.3
-
111
-
-
27944495588
-
Multiscale modeling of lipids and lipid bilayers
-
Lyubartsev, A. P. (2005). Multiscale modeling of lipids and lipid bilayers. European Biophysics Journal, 35, 53.
-
(2005)
European Biophysics Journal
, vol.35
, pp. 53
-
-
Lyubartsev, A.P.1
-
112
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodham, B., Reihar, W. E., III, Raux, B., Schlenjrich, M., Smith, J. C., Store, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., & Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B, 102, 3586.
-
(1998)
The Journal of Physical Chemistry B
, vol.102
, pp. 3586
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodham, B.19
Reihar III, W.E.20
Raux, B.21
Schlenjrich, M.22
Smith, J.C.23
Store, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
113
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004). Coarse grained model for semiquantitative lipid simulations. The Journal of Physical Chemistry B, 108, 750.
-
(2004)
The Journal of Physical Chemistry B
, vol.108
, pp. 750
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
114
-
-
34547474332
-
The MARTINI force field: Coarse grained model for biomolecular simulations
-
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007). The MARTINI force field: Coarse grained model for biomolecular simulations. The Journal of Physical Chemistry B, 111, 7812.
-
(2007)
The Journal of Physical Chemistry B
, vol.111
, pp. 7812
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
115
-
-
0000323669
-
Ab initio molecular dynamics: Theory and implementation
-
J. Grotendorst (Ed.), Julich: NIC, Accessed 02 July 2011
-
Marx, D., & Hutter, J. (2000). Ab initio molecular dynamics: Theory and implementation. In J. Grotendorst (Ed.), Modern methods and algorithms of quantum chemistry. Julich: NIC. http:// www.theochem.ruhr-uni-bochum.de/research/marx/marx.pdf. Accessed 02 July 2011.
-
(2000)
Modern methods and algorithms of quantum chemistry
-
-
Marx, D.1
Hutter, J.2
-
118
-
-
84925711387
-
Hoover NPT dynamics for systems varying in shape and size
-
Melchionna, S., Ciccotti, G., & Holian, B. L. (1993). Hoover NPT dynamics for systems varying in shape and size. Molecular Physics, 78, 533.
-
(1993)
Molecular Physics
, vol.78
, pp. 533
-
-
Melchionna, S.1
Ciccotti, G.2
Holian, B.L.3
-
119
-
-
0035903016
-
NSF launches TeraGrid for academic research
-
Mervis, J. (2001). NSF launches TeraGrid for academic research. Science, 293, 1235.
-
(2001)
Science
, vol.293
, pp. 1235
-
-
Mervis, J.1
-
120
-
-
84870061088
-
The pseudopotential plane wave approach
-
J. Grotendorst, S. Blugel, & D. Marx (Eds.), Julich: NIC, Accessed 02 July 2011
-
Meyer, B. (2006). The pseudopotential plane wave approach. In J. Grotendorst, S. Blugel, & D. Marx (Eds.), Computational nanoscience: Do it yourself! Julich: NIC. http://www2.fz- juelich.de/nic-series/volume31/meyer1.pdf. Accessed 02 July 2011.
-
(2006)
Computational nanoscience: Do it yourself!
-
-
Meyer, B.1
-
122
-
-
0002083815
-
Hybrid classical quantum force field for modeling very large molecules
-
Monard, G., Loos, M., Thery, V., Baka, K., & Rivail, J. L. (1996). Hybrid classical quantum force field for modeling very large molecules. International Journal of Quantum Chemistry, 58, 153.
-
(1996)
International Journal of Quantum Chemistry
, vol.58
, pp. 153
-
-
Monard, G.1
Loos, M.2
Thery, V.3
Baka, K.4
Rivail, J.L.5
-
123
-
-
1842816907
-
Special points for Brillouin-zone integrations
-
Monkhorst, H. J., & Pack, J. D. (1976). Special points for Brillouin-zone integrations. Physical Review B, 13, 5188.
-
(1976)
Physical Review B
, vol.13
, pp. 5188
-
-
Monkhorst, H.J.1
Pack, J.D.2
-
124
-
-
0000025086
-
Optimal meshes for integrals in real- and reciprocal-space unit cells
-
Moreno, J., & Soler, J. M. (1992). Optimal meshes for integrals in real- and reciprocal-space unit cells. Physical Review B, 45, 13891.
-
(1992)
Physical Review B
, vol.45
, pp. 13891
-
-
Moreno, J.1
Soler, J.M.2
-
125
-
-
0000125682
-
Frozen orbital QM/MM methods for density functional theory
-
Murphy, R. B., Philipp, D. M., & Friesner, R. A. (2000). Frozen orbital QM/MM methods for density functional theory. Chemical Physics Letters, 321, 113.
-
(2000)
Chemical Physics Letters
, vol.321
, pp. 113
-
-
Murphy, R.B.1
Philipp, D.M.2
Friesner, R.A.3
-
126
-
-
0037023160
-
A QM/MM approach with effective fragment potentials applied to the dipeptideaŁ“water structures
-
Nemukhin, A. V., Grigorenko, B. L., Bochenkova, A. V., Topol, I. A., & Burt, S. K. (2002). A QM/MM approach with effective fragment potentials applied to the dipeptideaŁ“water structures. Journal of Molecular Structure (THEOCHEM), 581, 167.
-
(2002)
Journal of Molecular Structure (THEOCHEM)
, vol.581
, pp. 167
-
-
Nemukhin, A.V.1
Grigorenko, B.L.2
Bochenkova, A.V.3
Topol, I.A.4
Burt, S.K.5
-
127
-
-
0041559813
-
-
Nemukhin, A. V., Grigorenko, B. L., Topol, I. A., & Burt, S. K. (2003). Journal of Computational Chemistry, 24, 1410.
-
(2003)
Journal of Computational Chemistry
, vol.24
, pp. 1410
-
-
Nemukhin, A.V.1
Grigorenko, B.L.2
Topol, I.A.3
Burt, S.K.4
-
128
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nose, S. (1984a). A unified formulation of the constant temperature molecular dynamics methods. Journal of Chemical Physics, 81, 511.
-
(1984)
Journal of Chemical Physics
, vol.81
, pp. 511
-
-
Nose, S.1
-
129
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nose, S. (1984b). A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52, 255.
-
(1984)
Molecular Physics
, vol.52
, pp. 255
-
-
Nose, S.1
-
130
-
-
85027363318
-
-
Accessed 02 July 2011
-
NWChem. (2008). http://www.nwchem-sw.org/index. php/Main_Page. Accessed 02 July 2011.
-
(2008)
-
-
-
131
-
-
85027357750
-
-
Accessed 02 July 2011
-
ONETEP. (2005). http://www2.tcm.phy.cam.ac.uk/onetep/. Accessed 02 July 2011.
-
(2005)
-
-
-
133
-
-
85027360126
-
-
Accessed 02 July 2011
-
Parrinello, M., Hutter, J., Marx, D., Focher, P., Tuckerman, M., Andreoni, W., Curioni, A., Fois, E., Roetlisberger, U., Giannozzi, P., Deutsch, T., Alavi, A., Sebastiani, D., Laio, A., Vande-Vondele, J., Seitsonen, A., & Billeter, S. (2008). Car-Parrinello molecular dynamics: An ab initio electronic structure and molecular dynamics program. http://www.cpmd.org. Accessed 02 July 2011.
-
(2008)
Car-Parrinello molecular dynamics: An ab initio electronic structure and molecular dynamics program
-
-
Parrinello, M.1
Hutter, J.2
Marx, D.3
Focher, P.4
Tuckerman, M.5
Andreoni, W.6
Curioni, A.7
Fois, E.8
Roetlisberger, U.9
Giannozzi, P.10
Deutsch, T.11
Alavi, A.12
Sebastiani, D.13
Laio, A.14
Vande-Vondele, J.15
Seitsonen, A.16
Billeter, S.17
-
134
-
-
0000337910
-
Theory of ab initio molecular-dynamics calculations
-
Pastore, G., Smargiassi, E., & Buda, F. (1991). Theory of ab initio molecular-dynamics calculations. Physical Review A44, 6334.
-
(1991)
Physical Review
, vol.A44
, pp. 6334
-
-
Pastore, G.1
Smargiassi, E.2
Buda, F.3
-
135
-
-
77958050495
-
-
Accessed 02 July 2011
-
PDB. (2010). RCSB protein data bank. http://www.rcsb.org/pdb. Accessed 02 July 2011.
-
(2010)
RCSB protein data bank
-
-
-
136
-
-
23244460838
-
Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation
-
Perdew, J. P., Chevary, J. A., Vosko, S. H., Jackson, K. A., Pederson, M. R., Singh, D. J., & Fiolhais, C. (1992). Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. Physical Review B, 46, 6671.
-
(1992)
Physical Review B
, vol.46
, pp. 6671
-
-
Perdew, J.P.1
Chevary, J.A.2
Vosko, S.H.3
Jackson, K.A.4
Pederson, M.R.5
Singh, D.J.6
Fiolhais, C.7
-
137
-
-
0001420061
-
Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
-
Philipp, D. M., & Friesner, R. A. (1999). Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. Journal of Computational Chemistry, 20, 1468.
-
(1999)
Journal of Computational Chemistry
, vol.20
, pp. 1468
-
-
Philipp, D.M.1
Friesner, R.A.2
-
138
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., Braun, R., Wang, W., Cumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., & Schulten, K. (2005a). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26, 1781.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1781
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Cumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
139
-
-
27344436659
-
-
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., & Schulten, K. (2005b). Journal of Computational Chemistry, 26, 1781.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1781
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
140
-
-
85027348803
-
-
Accessed 02 July 2011
-
PINY. (2005). http://homepages.nyu.edu/~mt33/PINY_MD/PINY.html. Accessed 02 July 2011.
-
(2005)
-
-
-
141
-
-
0002467378
-
Fast parallel algorithms for short-range molecular dynamics
-
Plimpton, S. J. (1995). Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117, 1.
-
(1995)
Journal of Computational Physics
, vol.117
, pp. 1
-
-
Plimpton, S.J.1
-
142
-
-
24844474404
-
An investigation of the importance of many-centre effects in the diatomicsin-molecules approach
-
Polak, R. (1986). An investigation of the importance of many-centre effects in the diatomicsin-molecules approach. Chemical Physics, 103, 277.
-
(1986)
Chemical Physics
, vol.103
, pp. 277
-
-
Polak, R.1
-
143
-
-
77749298172
-
Current status of the AMOEBA polarizable force field
-
Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., Jr., Head-Gordon, M., Clark, G. N. I., Johnson, M. E., & Head-Gordon, T. (2010). Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry B, 114, 2549.
-
(2010)
The Journal of Physical Chemistry B
, vol.114
, pp. 2549
-
-
Ponder, J.W.1
Wu, C.2
Ren, P.3
Pande, V.S.4
Chodera, J.D.5
Schnieders, M.J.6
Haque, I.7
Mobley, D.L.8
Lambrecht, D.S.9
DiStasio, R.A.10
Head-Gordon, M.11
Clark, G.N.I.12
Johnson, M.E.13
Head-Gordon, T.14
-
144
-
-
3142766126
-
Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with molecular mechanics by the Generalized Hybrid Orbital (GHO) method
-
Pu, J., Gao, J., & Truhlar, D. G. (2004a). Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with molecular mechanics by the Generalized Hybrid Orbital (GHO) method. The Journal of Physical Chemistry A, 108, 5454.
-
(2004)
The Journal of Physical Chemistry A
, vol.108
, pp. 5454
-
-
Pu, J.1
Gao, J.2
Truhlar, D.G.3
-
145
-
-
0442279531
-
Generalized Hybrid Orbital (GHO) method for combining ab initio Hartree-Fock wave functions with molecular mechanics
-
Pu, J., Gao, J., & Truhlar, D. G. (2004b). Generalized Hybrid Orbital (GHO) method for combining ab initio Hartree-Fock wave functions with molecular mechanics. The Journal of Physical Chemistry A, 108, 632.
-
(2004)
The Journal of Physical Chemistry A
, vol.108
, pp. 632
-
-
Pu, J.1
Gao, J.2
Truhlar, D.G.3
-
146
-
-
24944450993
-
Generalized Hybrid-Orbital method for combining density functional theory with molecular mechanicals
-
Pu, J., Gao, J., & Truhlar, D. G. (2005). Generalized Hybrid-Orbital method for combining density functional theory with molecular mechanicals. ChemPhysChem, 6, 1853.
-
(2005)
ChemPhysChem
, vol.6
, pp. 1853
-
-
Pu, J.1
Gao, J.2
Truhlar, D.G.3
-
147
-
-
84931507903
-
Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules I. Theory
-
Pulay, P. (1969). Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules I. Theory. Molecular Physics, 17, 197.
-
(1969)
Molecular Physics
, vol.17
, pp. 197
-
-
Pulay, P.1
-
148
-
-
84986524957
-
Convergence acceleration of iterative sequences. The case of SCF iteration
-
Pulay, P. (1980). Convergence acceleration of iterative sequences. The case of SCF iteration. Chemical Physics Letters, 73, 393.
-
(1980)
Chemical Physics Letters
, vol.73
, pp. 393
-
-
Pulay, P.1
-
149
-
-
44349162071
-
Improved SCF convergence acceleration
-
Pulay, P. (1982). Improved SCF convergence acceleration. Journal of Computational Chemistry, 3, 556.
-
(1982)
Journal of Computational Chemistry
, vol.3
, pp. 556
-
-
Pulay, P.1
-
150
-
-
85048704389
-
Analytical derivative methods in quantum chemistry
-
Pulay, P. (1987). Analytical derivative methods in quantum chemistry. Advances in Chemical Physics, 69, 241.
-
(1987)
Advances in Chemical Physics
, vol.69
, pp. 241
-
-
Pulay, P.1
-
151
-
-
85027328533
-
-
Accessed 02 July 2011
-
PWscf. (2009). http://www.pwscf.org/home.htm. Accessed 02 July 2011.
-
(2009)
-
-
-
152
-
-
85027375675
-
-
Accessed 02 July 2011
-
PyMOL. (2010). http://www.pymol.org. Accessed 02 July 2011.
-
(2010)
-
-
-
153
-
-
85027319004
-
-
Accessed 02 July 2011
-
QuantumEspresso. (2009). http://www.quantumespresso. org. Accessed 02 July 2011.
-
(2009)
-
-
-
154
-
-
85027381571
-
-
Accessed 02 July 2011
-
RasMol. (2008). http://rasmol.org/. Accessed 02 July 2011.
-
(2008)
-
-
-
156
-
-
0037250920
-
Grids, the TeraGrid, and beyond
-
Reed, D. A. (2003). Grids, the TeraGrid, and beyond. Computer, 36, 62.
-
(2003)
Computer
, vol.36
, pp. 62
-
-
Reed, D.A.1
-
157
-
-
0034635944
-
Moldy: A portable molecular dynamics simulation program for serial and parallel computers
-
Refson, K. (2000). Moldy: A portable molecular dynamics simulation program for serial and parallel computers. Computer Physics Communications, 126, 310.
-
(2000)
Computer Physics Communications
, vol.126
, pp. 310
-
-
Refson, K.1
-
158
-
-
0003872140
-
-
Accessed 02 July 2011
-
Refson, K. (2001). Moldy user’s manual. http://www.ccp5.ac.uk/moldy/moldy.html/. Accessed 02 July 2011.
-
(2001)
Moldy user’s manual
-
-
Refson, K.1
-
159
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W. R. P., Hunenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Kruger, P., & van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. The Journal of Physical Chemistry A, 103, 3596.
-
(1999)
The Journal of Physical Chemistry A
, vol.103
, pp. 3596
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
160
-
-
0037171005
-
First-principles simulation: Ideas, illustrations and the CASTEP code
-
Segall, M. D., Lindan, P. L. D., Probert, M. J., Pickard, C. J., Hasnip, P. J., Clark, S. J., & Payne, M. C. (2002). First-principles simulation: Ideas, illustrations and the CASTEP code. Journal of Physics: Condensed Matter, 14, 2717.
-
(2002)
Journal of Physics: Condensed Matter
, vol.14
, pp. 2717
-
-
Segall, M.D.1
Lindan, P.L.D.2
Probert, M.J.3
Pickard, C.J.4
Hasnip, P.J.5
Clark, S.J.6
Payne, M.C.7
-
162
-
-
0035846402
-
Simulations of phospholipids using a coarse grain model
-
Shelley, J. C., Shelley, M. Y., Reeder, R. C., Bandyopadhyay, S., Moore, P. B., & Klein, M. L. (2001). Simulations of phospholipids using a coarse grain model. The Journal of Physical Chemistry B, 105, 9785.
-
(2001)
The Journal of Physical Chemistry B
, vol.105
, pp. 9785
-
-
Shelley, J.C.1
Shelley, M.Y.2
Reeder, R.C.3
Bandyopadhyay, S.4
Moore, P.B.5
Klein, M.L.6
-
163
-
-
0037044173
-
Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations
-
Shillcock, J. C., & Lipowsky, R. (2002). Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations. Journal of Chemical Physics, 117, 5048.
-
(2002)
Journal of Chemical Physics
, vol.117
, pp. 5048
-
-
Shillcock, J.C.1
Lipowsky, R.2
-
164
-
-
0034623787
-
Screen savers of the world unite!
-
Shirts, M., & Pande, V. S. (2000). Screen savers of the world unite! Science, 290, 1903.
-
(2000)
Science
, vol.290
, pp. 1903
-
-
Shirts, M.1
Pande, V.S.2
-
165
-
-
84962477148
-
Structure/function correlations of enzymes using MM, QM/MM and related approaches; methods, concepts, Pitfalls and current progress
-
V. Dagett (Ed.), San Diego: Academic
-
Shurki, A., & Warshel, A. (2003). Structure/function correlations of enzymes using MM, QM/MM and related approaches; methods, concepts, Pitfalls and current progress. In V. Dagett (Ed.), Protein simulations, Adv. Protein Chem. (Vol. 66, p. 249). San Diego: Academic.
-
(2003)
Protein simulations, Adv. Protein Chem.
, vol.66
, pp. 249
-
-
Shurki, A.1
Warshel, A.2
-
166
-
-
85027367310
-
-
Accessed 02 July 2011
-
SIESTA. (2010). http://www.icmab.es/siesta/. Accessed 02 July 2011.
-
(2010)
-
-
-
167
-
-
34247616822
-
Extremely localized molecular orbitals: Theory and applications
-
Sironi, M., Genoni, A., Civera, M., Pieraccini, S., & Ghitti, M. (2007). Extremely localized molecular orbitals: Theory and applications. Theoretical Chemistry Accounts, 117, 685.
-
(2007)
Theoretical Chemistry Accounts
, vol.117
, pp. 685
-
-
Sironi, M.1
Genoni, A.2
Civera, M.3
Pieraccini, S.4
Ghitti, M.5
-
168
-
-
22944446425
-
Introducing ONETEP: Linear-scaling density functional simulations on parallel computers
-
Skylaris, C.-K., Haynes, P. D., Mostofi, A. A., & Payne, M. C. (2005). Introducing ONETEP: Linear-scaling density functional simulations on parallel computers. Journal of Chemical Physics, 122, 084119.
-
(2005)
Journal of Chemical Physics
, vol.122
-
-
Skylaris, C.-K.1
Haynes, P.D.2
Mostofi, A.A.3
Payne, M.C.4
-
169
-
-
0001603545
-
DL_POLY: Application to molecular simulation
-
Smith, W., Yong, C. W., & Rodger, P. M. (2002). DL_POLY: Application to molecular simulation. Molecular Simulation, 28, 385.
-
(2002)
Molecular Simulation
, vol.28
, pp. 385
-
-
Smith, W.1
Yong, C.W.2
Rodger, P.M.3
-
170
-
-
0037171091
-
The SIESTA method for ab initio order-N materials simulation
-
Soler, J. M., Artacho, E., Gale, J. D., Garcia, A., Junquera, J., Ordejon, P., & Sanchez-Portal, D. (2002). The SIESTA method for ab initio order-N materials simulation. Journal of Physics: Condensed Matter, 14, 2745.
-
(2002)
Journal of Physics: Condensed Matter
, vol.14
, pp. 2745
-
-
Soler, J.M.1
Artacho, E.2
Gale, J.D.3
Garcia, A.4
Junquera, J.5
Ordejon, P.6
Sanchez-Portal, D.7
-
171
-
-
85027346339
-
-
Accessed 02 July 2011
-
S/PHI/nX. (2009). http://www.mpie.de/index.php? id=sxlib. Accessed 02 July 2011.
-
(2009)
-
-
-
172
-
-
0000218559
-
Computer simulation of the dynamics of induced polarization fluctuations in water
-
Sprik, M. (1991). Computer simulation of the dynamics of induced polarization fluctuations in water. The Journal of Physical Chemistry, 95, 2283.
-
(1991)
The Journal of Physical Chemistry
, vol.95
, pp. 2283
-
-
Sprik, M.1
-
173
-
-
4243754961
-
Computer simulation of local order in condensed phases of silicon
-
Stillinger, F., & Weber, T. A. (1985). Computer simulation of local order in condensed phases of silicon. Physical Review B, 31, 5262.
-
(1985)
Physical Review B
, vol.31
, pp. 5262
-
-
Stillinger, F.1
Weber, T.A.2
-
174
-
-
0031644033
-
The COMPASS force field: Parameterization and validation for phosphazenes
-
Sun, H., Ren, P., & Fried, J. R. (1998). The COMPASS force field: Parameterization and validation for phosphazenes. Computational and Theoretical Polymer Science, 8, 229.
-
(1998)
Computational and Theoretical Polymer Science
, vol.8
, pp. 229
-
-
Sun, H.1
Ren, P.2
Fried, J.R.3
-
175
-
-
33646065526
-
Classical molecular dynamics
-
J. Grotendorst, D. Marx, & A. Muramatsu (Eds.), Julich: NIC, Accessed 02 July 2011
-
Sutmann, G. (2002). Classical molecular dynamics. In J. Grotendorst, D. Marx, & A. Muramatsu (Eds.), Quantum simulations of complex manybody systems: From theory to algorithms. Julich: NIC. http://www2.fz- juelich.de/nic-series/volume10/sutmann.pdf. Accessed 02 July 2011.
-
(2002)
Quantum simulations of complex manybody systems: From theory to algorithms
-
-
Sutmann, G.1
-
176
-
-
84928981412
-
Molecular dynamics - vision and reality
-
J. Grotendorst, S., Blugel, & D. Marx (Eds.), Julich: NIC, Accessed 02 July 2011
-
Sutmann, G. (2006). Molecular dynamics - vision and reality. In J. Grotendorst, S., Blugel, & D. Marx (Eds.), Computational nanoscience: Do it yourself! Julich: NIC. http://www2.fz- juelich.de/nic-series/volume31/sutmann.pdf. Accessed 02 July 2011.
-
(2006)
Computational nanoscience: Do it yourself!
-
-
Sutmann, G.1
-
177
-
-
36749110571
-
-
Swope, W. C., Anderson, H. C., Berens, P. H., & Wilson, K.R. (1982). Journal of Chemical Physics, 76, 637.
-
(1982)
Journal of Chemical Physics
, vol.76
, pp. 637
-
-
Swope, W.C.1
Anderson, H.C.2
Berens, P.H.3
Wilson, K.R.4
-
178
-
-
17444405896
-
A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties
-
Tepper, H. L., & Voth, G. A. (2005). A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties. Journal of Chemical Physics, 122, 124906.
-
(2005)
Journal of Chemical Physics
, vol.122
-
-
Tepper, H.L.1
Voth, G.A.2
-
179
-
-
16444366630
-
New empirical approach for the structure and energy of covalent systems
-
Tersoff, J. (1988). New empirical approach for the structure and energy of covalent systems. Physical Review B, 37, 6991.
-
(1988)
Physical Review B
, vol.37
, pp. 6991
-
-
Tersoff, J.1
-
180
-
-
27744577658
-
Modeling solid-state chemistry: Interatomic potentials for multicomponent systems
-
Tersoff, J. (1989). Modeling solid-state chemistry: Interatomic potentials for multicomponent systems. Physical Review B, 39, 5566.
-
(1989)
Physical Review B
, vol.39
, pp. 5566
-
-
Tersoff, J.1
-
181
-
-
84986492373
-
Quantum mechanical computations on very large molecular systems: The local self-consistent field method
-
Thery, V., Rinaldi, D., Rivail, J. L., Maigret, B., & Ferenczy, G. G. (1994). Quantum mechanical computations on very large molecular systems: The local self-consistent field method. Journal of Computational Chemistry, 15, 269.
-
(1994)
Journal of Computational Chemistry
, vol.15
, pp. 269
-
-
Thery, V.1
Rinaldi, D.2
Rivail, J.L.3
Maigret, B.4
Ferenczy, G.G.5
-
182
-
-
78349276203
-
QM/MM methodology: Fundamentals, scope, and limitations
-
J. Grotendorst, N. Attig, S. Blgel, & D. Marx (Eds.), Julich: NIC, Accessed 02 July 2011
-
Thiel, W. (2009). QM/MM methodology: Fundamentals, scope, and limitations. In J. Grotendorst, N. Attig, S. Blgel, & D. Marx (Eds.), Multiscale simulation methods in molecular sciences. Julich: NIC. http://www2.fz- juelich.de/nic-series/volume42/thiel.pdf. Accessed 02 July 2011.
-
(2009)
Multiscale simulation methods in molecular sciences
-
-
Thiel, W.1
-
184
-
-
0346539301
-
Ionic sizes and born repulsive parameters in the NaCl-type alkali halides II: The generalized Huggins-Mayer form
-
Tosi, M. P., & Fumi, F. G. (1964). Ionic sizes and born repulsive parameters in the NaCl-type alkali halides II: The generalized Huggins-Mayer form. Journal of Physics and Chemitry of Solids, 25, 45.
-
(1964)
Journal of Physics and Chemitry of Solids
, vol.25
, pp. 45
-
-
Tosi, M.P.1
Fumi, F.G.2
-
185
-
-
77952281190
-
-
Accessed 02 July 2011
-
Toth (2009). Information systems. http://www.tothcanada.com. Accessed 02 July 2011.
-
(2009)
Information systems
-
-
-
186
-
-
77957555616
-
Temperature control in molecular dynamic simulations of non-equilibrium processes
-
Toton, D., Lorenz, C. D., Rompotis, N., Martsinovich, N., & Kantorovich, L. (2010). Temperature control in molecular dynamic simulations of non-equilibrium processes. Journal of Physics Condensed Matter, 22, 074205.
-
(2010)
Journal of Physics Condensed Matter
, vol.22
-
-
Toton, D.1
Lorenz, C.D.2
Rompotis, N.3
Martsinovich, N.4
Kantorovich, L.5
-
188
-
-
0025431237
-
A straightforward method for generating soft transferable pseudopotentials
-
Troullier, N., & Martins, J. L. (1990). A straightforward method for generating soft transferable pseudopotentials. Solid State Communications, 74, 613.
-
(1990)
Solid State Communications
, vol.74
, pp. 613
-
-
Troullier, N.1
Martins, J.L.2
-
189
-
-
33645426115
-
Efficient pseudopotentials for plane-wave calculations
-
Troullier, N., & Martins, J. L. (1991). Efficient pseudopotentials for plane-wave calculations. Physical Review B, 43, 1993.
-
(1991)
Physical Review B
, vol.43
, pp. 1993
-
-
Troullier, N.1
Martins, J.L.2
-
190
-
-
33745113840
-
Path integration via molecular dynamics
-
J. Grotendorst, D. Marx, & A. Muramatsu (Eds.), Julich: NIC, Accessed 02 July 2011
-
Tuckerman, M. E. (2002). Path integration via molecular dynamics. In J. Grotendorst, D. Marx, & A. Muramatsu (Eds.), Quantum simulations of complex many-body systems: From theory to algorithms, Julich: NIC. http://www.fz- juelich.de/nic-series/volume10/tuckerman1.pdf. Accessed 02 July 2011.
-
(2002)
Quantum simulations of complex many-body systems: From theory to algorithms
-
-
Tuckerman, M.E.1
-
191
-
-
0002985201
-
Path integral molecular dynamics
-
B. J. Berne, G. Ciccotti, & D. F. Coker (Eds.), Singapore: World Scientific
-
Tuckerman, M. E., & Hughes, A. (1998). Path integral molecular dynamics. In B. J. Berne, G. Ciccotti, & D. F. Coker (Eds.), Classical and quantum dynamics in condensed phase simulations (p. 311). Singapore: World Scientific.
-
(1998)
Classical and quantum dynamics in condensed phase simulations
, pp. 311
-
-
Tuckerman, M.E.1
Hughes, A.2
-
192
-
-
36448999094
-
Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
-
Tuckerman, M. E., Berne, B. J., Martyna, G. J., & Klein, M. L. (1993). Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals. Journal of Chemical Physics, 99, 2796.
-
(1993)
Journal of Chemical Physics
, vol.99
, pp. 2796
-
-
Tuckerman, M.E.1
Berne, B.J.2
Martyna, G.J.3
Klein, M.L.4
-
193
-
-
11944254490
-
Force fields for silicas and aluminophosphates based on ab initio calculations
-
van Beest, B. W. H., Kramer, G. J., & van Santen, R. A. (1990). Force fields for silicas and aluminophosphates based on ab initio calculations. Physical Review Letters, 64, 1955.
-
(1990)
Physical Review Letters
, vol.64
, pp. 1955
-
-
Van Beest, B.W.H.1
Kramer, G.J.2
Van Santen, R.A.3
-
194
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005a). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1701
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
195
-
-
85027357145
-
-
Accessed 02 July 2011
-
van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A. R., Apol, E., Meulenhoff, P. J., Tieleman, D. P., Sijbers, A. L. T. M., Feenstra, K. A., van Drunen, R., & Berendsen, H. J. C. (2005b). Gromacs user manual version 4.0. http://www.gromacs.org/. Accessed 02 July 2011.
-
(2005)
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Van Buuren, A.R.4
Apol, E.5
Meulenhoff, P.J.6
Tieleman, D.P.7
Sijbers, A.L.T.M.8
Feenstra, K.A.9
Van Drunen, R.10
Berendsen, H.J.C.11
-
196
-
-
4243999855
-
Optimally smooth normconserving pseudopotentials
-
Vanderbilt, D. (1985). Optimally smooth normconserving pseudopotentials. Physical Review B, 32, 8412.
-
(1985)
Physical Review B
, vol.32
, pp. 8412
-
-
Vanderbilt, D.1
-
197
-
-
20544463457
-
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
-
Vanderbilt, D. (1990). Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Physical Review B, 41, 7892.
-
(1990)
Physical Review B
, vol.41
, pp. 7892
-
-
Vanderbilt, D.1
-
198
-
-
85027299091
-
-
Accessed 02 July 2011
-
Vanderbilt Ultra-Soft Pseudopotential Site. (2006). http://www.physics.rutgers.edu/~dhv/uspp/. Accessed 02 July 2011.
-
(2006)
-
-
-
199
-
-
15344345714
-
Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
-
VandeVondele, J., Krack, M., Mohamed, F., Parrinello, M., Chassaing, T., & Hutter, J. (2005). Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Computer Physics Communications, 167, 103.
-
(2005)
Computer Physics Communications
, vol.167
, pp. 103
-
-
VandeVondele, J.1
Krack, M.2
Mohamed, F.3
Parrinello, M.4
Chassaing, T.5
Hutter, J.6
-
200
-
-
33947289420
-
Large scale condensed matter calculations using the Gaussian and augmented plane waves method
-
Berlin/Heidelberg: Springer
-
VandeVondele, J., Iannuzzi, M., & Hutter, J. (2006). Large scale condensed matter calculations using the Gaussian and augmented plane waves method. In Computer simulations in condensed matter systems: From materials to chemical biology, Volume 1. Lecture notes in physics (Vol. 703, p. 287). Berlin/Heidelberg: Springer.
-
(2006)
Computer simulations in condensed matter systems: From materials to chemical biology, Volume 1. Lecture notes in physics
, vol.703
, pp. 287
-
-
VandeVondele, J.1
Iannuzzi, M.2
Hutter, J.3
-
201
-
-
85027346977
-
-
Accessed 02 July 2011
-
VASP. (2009). http://cms.mpi.univie.ac.at/vasp/. Accessed 02 July 2011.
-
(2009)
-
-
-
202
-
-
22944467757
-
Computer “Experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet, L. (1967). Computer “Experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Physical Review, 159, 98.
-
(1967)
Physical Review
, vol.159
, pp. 98
-
-
Verlet, L.1
-
203
-
-
85027314771
-
-
Accessed 02 July 2011
-
VMD. (2009). http://www.ks.uiuc.edu/Research/vmd/. Accessed 02 July 2011.
-
(2009)
-
-
-
204
-
-
0000216001
-
Accurate spin-dependent electron liquid correlation energies for local spin-density calculations - A critical analysis
-
Vosko, S. H., Wilk, L., & Nusair, M. (1980). Accurate spin-dependent electron liquid correlation energies for local spin-density calculations - A critical analysis. Canadian Journal of Physics, 58, 1200.
-
(1980)
Canadian Journal of Physics
, vol.58
, pp. 1200
-
-
Vosko, S.H.1
Wilk, L.2
Nusair, M.3
-
205
-
-
33645200462
-
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides
-
Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides. Journal of Computational Chemistry, 24, 1157.
-
(2004)
Journal of Computational Chemistry
, vol.24
, pp. 1157
-
-
Wang, J.M.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
207
-
-
0041876227
-
Computer simulations of enzyme catalysis: Methods, progress, and insights
-
Warshel, A. (2003). Computer simulations of enzyme catalysis: Methods, progress, and insights. Annual Review of Biophysics and Biomolecular Structure, 32, 425.
-
(2003)
Annual Review of Biophysics and Biomolecular Structure
, vol.32
, pp. 425
-
-
Warshel, A.1
-
208
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A., & Levitt, M. (1976). Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. Journal of Molecular Biology, 103, 227.
-
(1976)
Journal of Molecular Biology
, vol.103
, pp. 227
-
-
Warshel, A.1
Levitt, M.2
-
209
-
-
0003085787
-
Isothermal molecular dynamics calculations for liquid salts
-
Woodcock, L. V. (1971). Isothermal molecular dynamics calculations for liquid salts. Chemical Physics Letters, 10, 257.
-
(1971)
Chemical Physics Letters
, vol.10
, pp. 257
-
-
Woodcock, L.V.1
-
210
-
-
47549107229
-
Using the MCTDH wavepacket propagation method to describe multimode non-adiabatic dynamics
-
Worth, G. A., Meyer, H. D., Koeppel, H., Cederbaum, L. S., & Burghardt, I. (2008). Using the MCTDH wavepacket propagation method to describe multimode non-adiabatic dynamics. International Reviews in Physical Chemistry, 27, 569.
-
(2008)
International Reviews in Physical Chemistry
, vol.27
, pp. 569
-
-
Worth, G.A.1
Meyer, H.D.2
Koeppel, H.3
Cederbaum, L.S.4
Burghardt, I.5
-
211
-
-
22944472113
-
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
-
Zhang, Y. (2005). A pseudobond approach to combining quantum mechanical and molecular mechanical methods. Journal of Chemical Physics, 122, 024114.
-
(2005)
Journal of Chemical Physics
, vol.122
-
-
Zhang, Y.1
-
212
-
-
33748263629
-
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
-
Zhang, Y. (2006). Pseudobond ab initio QM/MM approach and its applications to enzyme reactions. Theoretical Chemistry Accounts, 116, 43.
-
(2006)
Theoretical Chemistry Accounts
, vol.116
, pp. 43
-
-
Zhang, Y.1
-
213
-
-
0001582558
-
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
-
Zhang, Y., Lee, T.-S., & Yang, W. (1999). A pseudobond approach to combining quantum mechanical and molecular mechanical methods. Journal of Chemical Physics, 110, 46.
-
(1999)
Journal of Chemical Physics
, vol.110
, pp. 46
-
-
Zhang, Y.1
Lee, T.-S.2
Yang, W.3
|