-
3
-
-
2442486484
-
A growing string method for determining transition states: Comparison to the nudged elastic band and string methods
-
Peters, B.; Heyden, A.; Bell A. T.; Chakraborty A. A growing string method for determining transition states: Comparison to the nudged elastic band and string methods. J. Chem. Phys. 2004, 120, 7877-7886.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 7877-7886
-
-
Peters, B.1
Heyden, A.2
Bell, A.T.3
Chakraborty, A.4
-
4
-
-
36849122972
-
High-temperature equation of state by a perturbation method, i. nonpolar gases
-
Zwanzig, R. W. High-temperature equation of state by a perturbation method, i. nonpolar gases. J. Chem. Phys. 1954, 22, 1420-1426.
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
5
-
-
0001626776
-
Adaptive umbrella sampling - Self-consistent determination of the nonboltzmann bias
-
Mezei, M. Adaptive umbrella sampling - self-consistent determination of the nonboltzmann bias. J. Comput. Phys. 1987, 68, 237-248.
-
(1987)
J. Comput. Phys.
, vol.68
, pp. 237-248
-
-
Mezei, M.1
-
7
-
-
0029633155
-
The calculation of the potential of mean force using computer simulations
-
Roux, B. The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun. 1995, 91, 275-282.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
8
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood, G. Statistical mechanics of fluid mixtures. J. Chem. Phys. 1935, 3, 300-313.
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 300-313
-
-
Kirkwood, G.1
-
9
-
-
0035935802
-
Calculating free energies using average force
-
Darve, E.; Pohorille, A. Calculating free energies using average force. J. Chem. Phys. 2001, 115, 9169-9183.
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 9169-9183
-
-
Darve, E.1
Pohorille, A.2
-
10
-
-
0042852135
-
Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
-
Gullingsrud, J. R.; Braun, R.; Schulten, K. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comput. Phys. 1999, 151, 190-211.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 190-211
-
-
Gullingsrud, J.R.1
Braun, R.2
Schulten, K.3
-
11
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
Jarzynski, C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 1997, 78, 2690-2693.
-
(1997)
Phys. Rev. Lett.
, vol.78
, pp. 2690-2693
-
-
Jarzynski, C.1
-
12
-
-
0012021417
-
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
-
Olender, R.; Elber, R. Calculation of classical trajectories with a very large time step: formalism and numerical examples. J. Chem. Phys. 1996, 105, 9299-9315.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 9299-9315
-
-
Olender, R.1
Elber, R.2
-
13
-
-
39249083909
-
Action-derived molecular dynamics in the study of rare events
-
No. 108302
-
Passerone, D.; Parrinello, M. Action-derived molecular dynamics in the study of rare events. Phys. Rev. Lett. 2001, 87, No. 108302.
-
(2001)
Phys. Rev. Lett.
, vol.87
-
-
Passerone, D.1
Parrinello, M.2
-
14
-
-
0000729781
-
Transition path sampling and the calculation of rate constants
-
Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition path sampling and the calculation of rate constants. J. Chem. Phys. 1998, 108, 1964-1977.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 1964-1977
-
-
Dellago, C.1
Bolhuis, P.G.2
Csajka, F.S.3
Chandler, D.4
-
15
-
-
0000106469
-
Multicanonical algorithms for 1st order phase-transitions
-
Berg, B. A.; Neuhaus, T. Multicanonical algorithms for 1st order phase-transitions. Phys. Lett. B 1991, 267, 249-253.
-
(1991)
Phys. Lett. B
, vol.267
, pp. 249-253
-
-
Berg, B.A.1
Neuhaus, T.2
-
16
-
-
0033688171
-
Temperature-accelarated dynamics for simulations of infrequent events
-
Sorensen, M. R.; Voter, A. F. Temperature-accelarated dynamics for simulations of infrequent events. J. Chem. Phys. 2000, 112, 9599-9606.
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 9599-9606
-
-
Sorensen, M.R.1
Voter, A.F.2
-
17
-
-
0037085922
-
On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
-
Rosso, L.; Minary, P.; Zhu, Z.; Tuckerman, M. E. On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles. J. Chem. Phys. 2002, 116, 4389-4402.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 4389-4402
-
-
Rosso, L.1
Minary, P.2
Zhu, Z.3
Tuckerman, M.E.4
-
18
-
-
0042378853
-
Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions
-
He, J.; Zhang, Z.; Shi, Y.; Liu, H. Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions. J. Chem. Phys. 2003, 119, 4005-4017.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 4005-4017
-
-
He, J.1
Zhang, Z.2
Shi, Y.3
Liu, H.4
-
19
-
-
0000087970
-
An adaptive umbrella sampling procedure in conformational-analysis using molecular dynamics and its application to glycol
-
Hooft, R. W. W.; Eijck, B. P. V.; Kroon, J. J. An adaptive umbrella sampling procedure in conformational-analysis using molecular dynamics and its application to glycol. J. Chem. Phys. 1992, 97, 6690-6694.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 6690-6694
-
-
Hooft, R.W.W.1
Eijck, B.P.V.2
Kroon, J.J.3
-
20
-
-
4344606960
-
Multidimensional adaptive umbrella sampling: Applications to main chain peptide conformations
-
Bartels, C.; Karplus, M. Multidimensional adaptive umbrella sampling: applications to main chain peptide conformations. J. Comput. Chem. 1997, 18, 1450-1462.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1450-1462
-
-
Bartels, C.1
Karplus, M.2
-
21
-
-
0028710015
-
Local elevation: A method for improving the searching properties of molecular dynamics simulation
-
Huber, T.; Torda, A. E.; van Gunsteren, W. F. Local elevation: A method for improving the searching properties of molecular dynamics simulation. J. Comput.-Aided Mol. Des. 1994, 8, 695-708.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 695-708
-
-
Huber, T.1
Torda, A.E.2
Van Gunsteren, W.F.3
-
22
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: Conformational flooding
-
Grubmüller, H. Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys. Rev. E 1995, 52, 2893-2906.
-
(1995)
Phys. Rev. E
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
23
-
-
6644221271
-
Efficient, multiple-range random walk algorithm to calculate the density of states
-
Wang, F.; Landau, D. P. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett. 2001, 86, 2050-2053.
-
(2001)
Phys. Rev. Lett.
, vol.86
, pp. 2050-2053
-
-
Wang, F.1
Landau, D.P.2
-
25
-
-
84888768692
-
-
See the Supporting Information for a current listing of papers on metadynamics applications
-
See the Supporting Information for a current listing of papers on metadynamics applications.
-
-
-
-
26
-
-
3042772813
-
Microscopic mechanism of antibiotics translocation through a porin
-
Ceccarelli, M.; Danelon, C.; Laio, A.; Parrinello, M. Microscopic mechanism of antibiotics translocation through a porin. Biophys. J. 2004, 87, 58-64.
-
(2004)
Biophys. J.
, vol.87
, pp. 58-64
-
-
Ceccarelli, M.1
Danelon, C.2
Laio, A.3
Parrinello, M.4
-
27
-
-
3242880241
-
Mapping potential energy surfaces
-
Wu, Y.; Schmitt, J. D.; Car, R. Mapping potential energy surfaces. J. Chem. Phys. 2004, 121, 1193-1200.
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 1193-1200
-
-
Wu, Y.1
Schmitt, J.D.2
Car, R.3
-
28
-
-
14744276066
-
Flexible docking in solution using metadynamics
-
Gervasio, F. L.; Laio, A.; Parrinello, M. Flexible docking in solution using metadynamics. J. Am. Chem. Soc. 2005, 127, 2600-2607.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 2600-2607
-
-
Gervasio, F.L.1
Laio, A.2
Parrinello, M.3
-
29
-
-
0041810451
-
Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics
-
No. 238302
-
Iannuzzi, M.; Laio, A.; Parrinello, M. Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics. Phys. Rev. Lett. 2003, 90, No. 238302.
-
(2003)
Phys. Rev. Lett.
, vol.90
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
31
-
-
0037458399
-
Predicting crystal structures: The Parrinello-Rahman method revisited
-
No. 075503
-
Martoñák, R.; Laio, A.; Parrinello, M. Predicting crystal structures: the Parrinello-Rahman method revisited. Phys. Rev. Lett. 2003, 90, No. 075503.
-
(2003)
Phys. Rev. Lett.
, vol.90
-
-
Martoñák, R.1
Laio, A.2
Parrinello, M.3
-
32
-
-
17144380812
-
Topological defects and bulk melting of hexagonal ice
-
Donadio, D.; Raiteri, P.; Parrinello, M. Topological defects and bulk melting of hexagonal ice. J. Phys. Chem. B 2005, 109, 5421-5424.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 5421-5424
-
-
Donadio, D.1
Raiteri, P.2
Parrinello, M.3
-
33
-
-
2942548219
-
Reconstructing the density of states by history-dependent metadynamics
-
No. 170601
-
Micheletti, C.; Laio, A.; Parrinello, M. Reconstructing the density of states by history-dependent metadynamics. Phys. Rev. Lett. 2004, 92, No. 170601.
-
(2004)
Phys. Rev. Lett.
, vol.92
-
-
Micheletti, C.1
Laio, A.2
Parrinello, M.3
-
34
-
-
17444362272
-
A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions
-
Ensing, B.; Laio, A.; Parrinello, M.; Klein, M. L. A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. J. Phys. Chem. B 2005, 109, 6676.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6676
-
-
Ensing, B.1
Laio, A.2
Parrinello, M.3
Klein, M.L.4
-
35
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, R. L.; Dunbrack, R. L., Jr.; 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.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, R.L.3
Dunbrack Jr., 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
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
37
-
-
4243606192
-
Unified approach for molecular dynamics and density-functional theory
-
Car, R.; Parrinello, M. Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 1985, 55, 2471-2474.
-
(1985)
Phys. Rev. Lett.
, vol.55
, pp. 2471-2474
-
-
Car, R.1
Parrinello, M.2
-
38
-
-
0036286854
-
The role and perspective of ab initio molecular dynamics in the study of biological systems
-
Carloni, P.; Rothlisberger, U.; Parrinello, M. The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc. Chem. Res. 2002, 35, 455-464.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 455-464
-
-
Carloni, P.1
Rothlisberger, U.2
Parrinello, M.3
-
39
-
-
17444412296
-
Assessing the accuracy of metadynamics
-
Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. Assessing the accuracy of metadynamics. J. Phys. Chem. B 2005, 109, 6714-6721.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6714-6721
-
-
Laio, A.1
Rodriguez-Fortea, A.2
Gervasio, F.L.3
Ceccarelli, M.4
Parrinello, M.5
-
40
-
-
33845379042
-
N2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
-
N2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution. J. Am. Chem. Soc. 1985, 107, 154-163.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 154-163
-
-
Chandrasekhar, J.1
Smith, S.F.2
Jorgensen, W.L.3
-
41
-
-
0035810446
-
-, in water
-
-, in water. J. Phys. Chem. A 2001, 105, 3300-3310.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 3300-3310
-
-
Ensing, B.1
Meijer, E.J.2
Blöchl, P.E.3
Baerends, E.J.4
-
42
-
-
0342809856
-
Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: A comparison of theoretical results
-
Tobias, D. J.; Brooks, C. L., III Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results. J. Phys. Chem. 1992, 96, 3864-3870.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 3864-3870
-
-
Tobias, D.J.1
Brooks III, C.L.2
-
43
-
-
0001102309
-
The alanine dipeptide free energy surface in solution
-
Smith, P. E. The alanine dipeptide free energy surface in solution. J. Chem. Phys. 1999, 111, 5568-5579.
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 5568-5579
-
-
Smith, P.E.1
-
44
-
-
0001568871
-
Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
-
Apostolakis, J.; Ferrara, P.; Caflish, A. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water. J. Chem. Phys. 1999, 110, 2099-2108.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 2099-2108
-
-
Apostolakis, J.1
Ferrara, P.2
Caflish, A.3
-
45
-
-
15544386773
-
Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics
-
Rosso, L.; Abrams, J. B.; Tuckerman, M. E. Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics. J. Phys. Chem. B 2005, 109, 4162-4167.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 4162-4167
-
-
Rosso, L.1
Abrams, J.B.2
Tuckerman, M.E.3
-
46
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400-1415.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
|