- 1
-
D. Frenkel and B. Smit.
Understanding Molecular Simulation: From Algorithms to
Applications.
Academic Press, San Diego, 2 edition, 2002.
- 2
-
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
- 3
-
Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth, Augusta H.
Teller, and Edward Teller.
Equation of state calculations by fast computing machines.
The Journal of Chemical Physics, 21(6):1087-1092, 1953.
- 4
-
Loup Verlet.
Computer "Experiments" on Classical Fluids. I. Thermodynamical
Properties of Lennard-Jones Molecules.
Physical Review, 159(1):98-103, 7 1967.
- 5
-
William C. Swope, Hans C. Andersen, Peter H. Berens, and Kent R. Wilson.
A computer simulation method for the calculation of equilibrium
constants for the formation of physical clusters of molecules: Application to
small water clusters.
The Journal of Chemical Physics, 76(1):637-649, 1982.
- 6
-
M. Tuckerman, B. J. Berne, and G. J. Martyna.
Reversible multiple time scale molecular dynamics.
The Journal of Chemical Physics, 97(3):1990, 1992.
- 7
-
H. Flyvbjerg and H. G. Petersen.
Error estimates on averages of correlated data.
The Journal of Chemical Physics, 91(1):461-466, 1989.
- 8
-
Edward J. Maginn, Richard A. Messerly, Daniel J. Carlson, Daniel R. Roe, and
J. Richard Elliott.
Best Practices for Computing Transport Properties 1.
Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article
v1.0].
Living Journal of Computational Molecular Science, 1(1):1-20,
2019.
- 9
-
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R.
Haak.
Molecular dynamics with coupling to an external bath.
The Journal of Chemical Physics, 81(8):3684-3690, 10 1984.
- 10
-
Hans C. Andersen.
Molecular dynamics simulations at constant pressure and/or
temperature.
The Journal of Chemical Physics, 72(1980):2384, 1980.
- 11
-
GS Grest and K Kremer.
Structure of many arm star polymers: a molecular dynamics
simulation.
Macromolecules, 20:1376-1383, 1987.
- 12
-
P Nikunen.
How would you integrate the equations of motion in dissipative
particle dynamics simulations?
Computer Physics Communications, 153(3):407-423, 7 2003.
- 13
-
Thomas Soddemann, Burkhard Dünweg, and Kurt Kremer.
Dissipative particle dynamics: A useful thermostat for equilibrium
and nonequilibrium molecular dynamics simulations.
Physical Review E, 68(4):1-8, 10 2003.
- 14
-
P. P. Ewald.
Die Berechnung optischer und elektrostatischer Gitterpotentiale.
Annalen der Physik, 369(3):253-287, 1921.
- 15
-
Markus Deserno and Christian Holm.
How to mesh up Ewald sums. I. A theoretical and numerical comparison
of various particle mesh routines.
The Journal of chemical physics, 109(18):7678, 1998.
- 16
-
Markus Deserno.
3 Efficient electrostatics : Ewald Sum and Particle Mesh Ewald
Algorithms.
PhD thesis, 1999.
- 17
-
Judith A. Harrison, J. David Schall, Sabina Maskey, Paul T. Mikulski, M. Todd
Knippenberg, and Brian H. Morrow.
Review of force fields and intermolecular potentials used in
atomistic computational materials research.
Applied Physics Reviews, 5(3), 2018.
- 18
-
Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States,
S. Swaminathan, and Martin Karplus.
CHARMM: A program for macromolecular energy, minimization, and
dynamics calculations.
Journal of Computational Chemistry, 4(2):187-217, 1983.
- 19
-
B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella,
B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves,
Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im,
K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B.
Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu,
W. Yang, D. M. York, and M. Karplus.
CHARMM: The biomolecular simulation program.
Journal of Computational Chemistry, 30(10):1545-1614, 7 2009.
- 20
-
A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J.
Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir,
K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen,
B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote,
J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus.
All-Atom Empirical Potential for Molecular Modeling and Dynamics
Studies of Proteins †.
The Journal of Physical Chemistry B, 102(18):3586-3616, 4
1998.
- 21
-
Paul K. Weiner and Peter A. Kollman.
AMBER: Assisted model building with energy refinement. A general
program for modeling molecules and their interactions.
Journal of Computational Chemistry, 2(3):287-303, 1981.
- 22
-
Xavier Daura, Alan E. Mark, and Wilfred F. Van Gunsteren.
Parametrization of aliphatic CHn united atoms of GROMOS96 force
field.
Journal of Computational Chemistry, 19(5):535-547, 1998.
- 23
-
William L. Jorgensen, Jeffry D. Madura, and Carol J. Swenson.
Optimized Intermolecular Potential Functions for Liquid
Hydrocarbons.
Journal of the American Chemical Society, 106(22):6638-6646,
1984.
- 24
-
William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives.
Development and testing of the OPLS all-atom force field on
conformational energetics and properties of organic liquids.
Journal of the American Chemical Society, 118(45):11225-11236,
1996.
- 25
-
Marcus G. Martin and J. Ilja Siepmann.
Transferable potentials for phase equilibria. 1. United-atom
description of n-alkanes.
Journal of Physical Chemistry B, 102(14):2569-2577, 1998.
- 26
-
Pedro E.M. Lopes, Benoit Roux, and Alexander D. MacKerell.
Molecular modeling and dynamics studies with explicit inclusion of
electronic polarizability: Theory and applications.
Theoretical Chemistry Accounts, 124(1-2):11-28, 2009.
- 27
-
K. Vanommeslaeghe and A. D. Mackerell.
CHARMM additive and polarizable force fields for biophysics and
computer-aided drug design.
Biochimica et Biophysica Acta - General Subjects,
1850(5):861-871, 2015.
- 28
-
Murray S. Daw and M. I. Baskes.
Embedded-atom method: Derivation and application to impurities,
surfaces, and other defects in metals.
Physical Review B, 29(12):6443-6453, 1984.
- 29
-
Cameron F. Abrams and David B. Graves.
Three-dimensional spatiokinetic distributions of sputtered and
scattered products of Ar+ and Cu+ impacts onto the Cu surface: Molecular
dynamics simulations.
IEEE Transactions on Plasma Science, 27(5):1426-1432, 1999.
- 30
-
G. C. Abell.
Empirical chemical pseudopotential theory of molecular and metallic
bonding.
Physical Review B, 31(10):6184-6196, 5 1985.
- 31
-
J. Tersoff.
New empirical model for the structural properties of silicon.
Physical Review Letters, 56(6):632-635, 2 1986.
- 32
-
Donald W. Brenner.
Empirical potential for hydrocarbons for use in simulating the
chemical vapor deposition of diamond films.
Physical Review B, 42(15):9458-9471, 1990.
- 33
-
Steven J. Stuart, Alan B. Tutein, and Judith A. Harrison.
A reactive potential for hydrocarbons with intermolecular
interactions.
Journal of Chemical Physics, 112(14):6472-6486, 2000.
- 34
-
Jianguo Yu, Susan B. Sinnott, and Simon R. Phillpot.
Charge optimized many-body potential for the Si/SiO2 system.
Physical Review B - Condensed Matter and Materials Physics,
75(8):1-13, 2007.
- 35
-
M Todd Knippenberg, Paul T Mikulski, Kathleen E Ryan, Steven J Stuart, Guangtu
Gao, and Judith A Harrison.
Bond-order potentials with split-charge equilibration: Application
to C-, H-, and O-containing systems.
The Journal of Chemical Physics, 136(16):164701, 4 2012.
- 36
-
Thomas P. Senftle, Sungwook Hong, Md Mahbubul Islam, Sudhir B. Kylasa, Yuanxia
Zheng, Yun Kyung Shin, Chad Junkermeier, Roman Engel-Herbert, Michael J.
Janik, Hasan Metin Aktulga, Toon Verstraelen, Ananth Grama, and Adri C.T.
Van Duin.
The ReaxFF reactive force-field: Development, applications and
future directions.
npj Computational Materials, 2(September 2015), 2016.
- 37
-
Michael F. Russo and Adri C.T. van Duin.
Atomistic-scale simulations of chemical reactions: Bridging from
quantum chemistry to engineering.
Nuclear Instruments and Methods in Physics Research Section B:
Beam Interactions with Materials and Atoms, 269(14):1549-1554, 7 2011.
- 38
-
F.H. Stillinger and T.A. Weber.
Computer simulation of local order in condensed phases of silicon.
Physical Review B, 31(8):5262, 1985.
- 39
-
H BEKKER, HJC BERENDSEN, EJ DIJKSTRA, S ACHTEROP, R VONDRUMEN, D VANDERSPOEL,
A SIJBERS, H Keegstra, and MKR RENARDUS.
Gromacs - a parallel computer for molecular-dynamics simulations.
In RA DeGroot and J Nadrchal, editors, PHYSICS COMPUTING '92,
pages 252-256. World Scientific Publishing, 1993.
4th International Conference on Computational Physics (PC 92) ;
Conference date: 24-08-1992 Through 28-08-1992.
- 40
-
James C Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid,
Elizabeth Villa, Christophe Chipot, Robert D Skeel, Laxmikant Kalé, and
Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of computational chemistry, 26(16):1781-802, 12 2005.
- 41
-
Kefang Liu, Shuguang Tan, Sheng Niu, Jia Wang, Lili Wu, Huan Sun, Yanfang
Zhang, Xiaoqian Pan, Xiao Qu, Pei Du, Yumin Meng, Yunfei Jia, Qian Chen,
Chuxia Deng, Jinghua Yan, Hong-Wei Wang, Qihui Wang, Jianxun Qi, and
George Fu Gao.
Cross-species recognition of SARS-CoV-2 to bat ACE2.
Proceedings of the National Academy of Sciences,
118(1):e2020216118, 1 2021.
- 42
-
Cameron Abrams and Giovanni Bussi.
Enhanced Sampling in Molecular Dynamics Using Metadynamics,
Replica-Exchange, and Temperature-Acceleration.
Entropy, 16(1):163-199, 12 2013.
- 43
-
Ilario G. Tironi and Wilfred F. Van Gunsteren.
A molecular dynamics simulation study of chloroform.
Molecular Physics, 83(2):381-403, 10 1994.
- 44
-
Charles H. Bennett.
Efficient estimation of free energy differences from Monte Carlo
data.
Journal of Computational Physics, 22(2):245-268, 1976.
- 45
-
Shankar Kumar, John M Rosenberg, Djamal Bouzida, Robert H Swendsen, and Peter A
Kollman.
THE weighted histogram analysis method for free-energy calculations
on biomolecules. I. The method.
Journal of Computational Chemistry, 13(8):1011-1021, 1992.
- 46
-
Giovanni Bussi and Alessandro Laio.
Using metadynamics to explore complex free-energy landscapes.
Nature Reviews Physics, 2(4):200-212, 2020.
- 47
-
Jeffrey Comer, James C. Gumbart, Jérôme Hénin, Tony Lelievre, Andrew
Pohorille, and Christophe Chipot.
The adaptive biasing force method: Everything you always wanted to
know but were afraid to ask.
Journal of Physical Chemistry B, 119(3):1129-1151, 2015.
- 48
-
Alessandro Laio and Michele Parrinello.
Escaping free-energy minima.
Proceedings of the National Academy of Sciences of the United
States of America, 99(20):12562-6, 10 2002.
- 49
-
Alessandro Barducci, Giovanni Bussi, and Michele Parrinello.
Well-tempered metadynamics: A smoothly converging and tunable
free-energy method.
Physical Review Letters, 100(2):1-4, 2008.
cfa22@drexel.edu