-
1
-
-
84875801065
-
-
Gromos-87 manual, Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands
-
van Gunsteren WF, Berendsen HJC. Gromos-87 manual, Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.
-
(1987)
-
-
van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
2
-
-
46249092554
-
Gromacs 4.0: algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E. Gromacs 4.0: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008, 4:435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
3
-
-
73949107784
-
Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supercomputer
-
Schulz R, Lindner B, Petridis L, Smith JC. Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supercomputer. J Chem Theory Comput 2009, 5:2798-2808.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2798-2808
-
-
Schulz, R.1
Lindner, B.2
Petridis, L.3
Smith, J.C.4
-
4
-
-
77956286977
-
GPU-accelerated molecular modeling coming of age
-
Stone JE, Hardy DJ, Ufimtsev IS, Schulten K. GPU-accelerated molecular modeling coming of age. J Mol Graph Model 2010, 29:116-125.
-
(2010)
J Mol Graph Model
, vol.29
, pp. 116-125
-
-
Stone, J.E.1
Hardy, D.J.2
Ufimtsev, I.S.3
Schulten, K.4
-
5
-
-
84862813004
-
Algorithm improvements for molecular dynamics simulations
-
DOI: 10.1002/wcms.3
-
Larsson P, Hess B, Lindahl E. Algorithm improvements for molecular dynamics simulations. Comput. Molec. Sci. 1 (2011) DOI: 10.1002/wcms.3.
-
(2011)
Comput. Molec. Sci.
, vol.1
-
-
Larsson, P.1
Hess, B.2
Lindahl, E.3
-
6
-
-
36949017804
-
A molecular dynamics study of polarizable water
-
Ahlström P, Wallqvist A, Engström S, Jönsson B. A molecular dynamics study of polarizable water. Mol Phys 1989, 68:563-581.
-
(1989)
Mol Phys
, vol.68
, pp. 563-581
-
-
Ahlström, P.1
Wallqvist, A.2
Engström, S.3
Jönsson, B.4
-
7
-
-
0343867257
-
A mobile charge densities in harmonic oscillators MCDHO molecular model for numerical simulation: the water-water interaction
-
Saint-Martin H, Hernández-Cobos J, Bernal-Uruchurtu MI, Ortega- Blake I, Berendsen HJC. A mobile charge densities in harmonic oscillators MCDHO molecular model for numerical simulation: the water-water interaction. J Chem Phys 2000, 113:10899-10912.
-
(2000)
J Chem Phys
, vol.113
, pp. 10899-10912
-
-
Saint-Martin, H.1
Hernández-Cobos, J.2
Bernal-Uruchurtu, M.I.3
Ortega-Blake, I.4
Berendsen, H.J.C.5
-
8
-
-
0035810439
-
Molecular dynamics simulations of water with a novel shell-model potential
-
van Maaren PJ, van der Spoel D. Molecular dynamics simulations of water with a novel shell-model potential. J Phys Chem B 2001, 105: 2618-2626.
-
(2001)
J Phys Chem B
, vol.105
, pp. 2618-2626
-
-
van Maaren, P.J.1
van der Spoel, D.2
-
9
-
-
0037260956
-
Development of a simple, self- consistent polarizable model for liquid water
-
Yu HB, Hansson T, van Gunsteren WF. Development of a simple, self- consistent polarizable model for liquid water. J Chem Phys 2003, 118:221-234.
-
(2003)
J Chem Phys
, vol.118
, pp. 221-234
-
-
Yu, H.B.1
Hansson, T.2
van Gunsteren, W.F.3
-
10
-
-
0041878923
-
Modeling induced polarization with classical drude oscillators: theory and molecular dynamics simulation algorithm
-
Lamoureux G, Roux B. Modeling induced polarization with classical drude oscillators: theory and molecular dynamics simulation algorithm. J Chem Phys 2003, 119:3025-3039.
-
(2003)
J Chem Phys
, vol.119
, pp. 3025-3039
-
-
Lamoureux, G.1
Roux, B.2
-
11
-
-
77956241004
-
Polarizable empirical force field for sulfur-containing compounds based on the classical drude oscillator model
-
Zhu X, Mackerell AD Jr. Polarizable empirical force field for sulfur-containing compounds based on the classical drude oscillator model. J Comput Chem 2010, 31:2330-2341.
-
(2010)
J Comput Chem
, vol.31
, pp. 2330-2341
-
-
Zhu, X.1
Mackerell Jr., A.D.2
-
12
-
-
77749298172
-
Current status of the AMOEBA polarizable force field
-
Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA Jr, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B 2010, 114:2549-2564.
-
(2010)
J Phys Chem B
, vol.114
, pp. 2549-2564
-
-
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 Jr., R.A.10
-
13
-
-
77950180192
-
Gaussian multipole model GMM
-
Elking DM, Cisneros GA, Piquemal J-P, Darden TA, Pedersen LG. Gaussian multipole model GMM. J Chem Theory Comput 2010, 6:190-202.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 190-202
-
-
Elking, D.M.1
Cisneros, G.A.2
Piquemal, J.-P.3
Darden, T.A.4
Pedersen, L.G.5
-
14
-
-
34250124408
-
The approximation of electron densities
-
Smith CM, Hall GG. The approximation of electron densities. Theor Chim Acta 1986, 69:63-69.
-
(1986)
Theor Chim Acta
, vol.69
, pp. 63-69
-
-
Smith, C.M.1
Hall, G.G.2
-
15
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E, Hess BA, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001, 7:306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.A.2
van der Spoel, D.3
-
16
-
-
0035504327
-
Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates Q-hop MD
-
Lill MA, Helms V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates Q-hop MD. J Chem Phys 2001, 115:7993-8005.
-
(2001)
J Chem Phys
, vol.115
, pp. 7993-8005
-
-
Lill, M.A.1
Helms, V.2
-
17
-
-
0034699054
-
A universal approach to web-based chemistry using XML and CML
-
Murray-Rust P, Rzepa HS, Wright M, Zara S. A universal approach to web-based chemistry using XML and CML. Chem Comm 2000, 16:1471-1472.
-
(2000)
Chem Comm
, vol.16
, pp. 1471-1472
-
-
Murray-Rust, P.1
Rzepa, H.S.2
Wright, M.3
Zara, S.4
-
18
-
-
77955486396
-
Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails
-
Kasson PM, Lindahl E, Pande VS. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput Biol 2010, 6:1-8.
-
(2010)
PLoS Comput Biol
, vol.6
, pp. 1-8
-
-
Kasson, P.M.1
Lindahl, E.2
Pande, V.S.3
-
19
-
-
78149457466
-
A method for interaction rescaling to enable high-performance tabulated generalized born simulations
-
Larsson P, Lindahl E. A method for interaction rescaling to enable high-performance tabulated generalized born simulations. J Comput Chem 2010, 31:2593-2600.
-
(2010)
J Comput Chem
, vol.31
, pp. 2593-2600
-
-
Larsson, P.1
Lindahl, E.2
-
20
-
-
85008042563
-
A hardware-independent framework for molecular simulations
-
Eastman P, Pande VS, Open MM. A hardware-independent framework for molecular simulations. Comput Sci Eng 2010, 12:34-39.
-
(2010)
Comput Sci Eng
, vol.12
, pp. 34-39
-
-
Eastman, P.1
Pande, V.S.2
Open, M.M.3
-
21
-
-
34547474332
-
The MARTINI force field: coarse grained model for biomolecular simulations
-
Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 2007, 111:7812-7824.
-
(2007)
J Phys Chem B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
de Vries, A.H.5
-
23
-
-
0142180089
-
Dynamic properties of water/alcohol mixtures studied by computer simulation
-
Wensink EJW, Hoffmann AC, van Maaren PJ, van der Spoel D. Dynamic properties of water/alcohol mixtures studied by computer simulation. J Chem Phys 2003, 119:7308-7317.
-
(2003)
J Chem Phys
, vol.119
, pp. 7308-7317
-
-
Wensink, E.J.W.1
Hoffmann, A.C.2
van Maaren, P.J.3
van der Spoel, D.4
-
24
-
-
33645678321
-
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
-
van der Spoel D, van Maaren PJ, Larsson P, Tîmneanu N. Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media. J Phys Chem B 2006, 110:4393-4398.
-
(2006)
J Phys Chem B
, vol.110
, pp. 4393-4398
-
-
van der Spoel, D.1
van Maaren, P.J.2
Larsson, P.3
Tîmneanu, N.4
-
25
-
-
0017100947
-
Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme
-
Warshel A, Levitt M. Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol 1976, 103:227-249.
-
(1976)
J Mol Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
26
-
-
77950584902
-
Software news and update reconstruction of atomistic details from coarse-grained structures
-
Rzepiela AJ, Schafer LV, Goga N, Risselada HJ, De Vries AH, Marrink SJ. Software news and update reconstruction of atomistic details from coarse-grained structures. J Comput Chem 2010, 31:1333-1343.
-
(2010)
J Comput Chem
, vol.31
, pp. 1333-1343
-
-
Rzepiela, A.J.1
Schafer, L.V.2
Goga, N.3
Risselada, H.J.4
De Vries, A.H.5
Marrink, S.J.6
-
27
-
-
34547926023
-
Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
-
Christen M, van Gunsteren W. Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. J Chem Phys 2006, 124:154106.
-
(2006)
J Chem Phys
, vol.124
, pp. 154106
-
-
Christen, M.1
van Gunsteren, W.2
-
28
-
-
41049093757
-
Multiscale simulation of soft matter: from scale bridging to adaptive resolution
-
Praprotnik M, Delle Site L, Kremer K. Multiscale simulation of soft matter: from scale bridging to adaptive resolution. Annu Rev Phys Chem 2008, 59:545-571.
-
(2008)
Annu Rev Phys Chem
, vol.59
, pp. 545-571
-
-
Praprotnik, M.1
Delle Site, L.2
Kremer, K.3
-
29
-
-
70449467178
-
Multiscale simulation of soft matter systems-from the atomistic to the coarse-grained level and back
-
Peter C, Kremer K. Multiscale simulation of soft matter systems-from the atomistic to the coarse-grained level and back. Soft Matter 2009, 5:4357-4366.
-
(2009)
Soft Matter
, vol.5
, pp. 4357-4366
-
-
Peter, C.1
Kremer, K.2
-
30
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988, 110:1657-1666.
-
(1988)
J Am Chem Soc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
31
-
-
0026372584
-
Molecular-dynamics simulations on distributed memory machines
-
Liem S, Brown D, Clarke J. Molecular-dynamics simulations on distributed memory machines. Comput Phys Commun 1991, 67:261-267.
-
(1991)
Comput Phys Commun
, vol.67
, pp. 261-267
-
-
Liem, S.1
Brown, D.2
Clarke, J.3
-
32
-
-
24144495573
-
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
-
Shaw DE. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comp Chem 2005, 26:1318-1328.
-
(2005)
J Comp Chem
, vol.26
, pp. 1318-1328
-
-
Shaw, D.E.1
-
33
-
-
0029011701
-
A second generation force field for the simulation of proteins and nucleic acids
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz-Jr KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc 1995, 117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz-Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
34
-
-
4444351490
-
Empirical force fields for biological macromolecules: overview and issues
-
Mackerell A. Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 2004, 25:1584-1604.
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
Mackerell, A.1
-
35
-
-
77950106854
-
Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models
-
Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E. Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models. J Chem Theory Comput 2010, 6:459-466.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 459-466
-
-
Bjelkmar, P.1
Larsson, P.2
Cuendet, M.A.3
Hess, B.4
Lindahl, E.5
-
36
-
-
38749123962
-
P-LINCS: a parallel linear constraint solver for molecular simulation
-
Hess B. P-LINCS: a parallel linear constraint solver for molecular simulation. J Chem Theory Comput 2008, 4:116-122.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
37
-
-
0001585978
-
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
-
Feenstra KA, Hess B, Berendsen HJC. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J Comp Chem 1999, 20:786-798.
-
(1999)
J Comp Chem
, vol.20
, pp. 786-798
-
-
Feenstra, K.A.1
Hess, B.2
Berendsen, H.J.C.3
|