scholarly journals New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8432-8449 ◽  
Author(s):  
Jejoong Yoo ◽  
Aleksei Aksimentiev
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Biomolecular Systems ◽  
Recent Advances ◽  
Dynamics Simulations

Recent advances in parallel computing have pushed all-atom molecular dynamics simulations into an untested territory. This article reviews the applications of the NBFIX approach for testing and improving molecular dynamics force fields and discuses the implications of the NBFIX corrections for simulations of various biomolecular systems.

How to Assign AMBER Parameters to Desmond-generated System with viparr4 v1

2021 ◽  
Author(s):  
Thilo Mast ◽  
Dmitry Lupyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Third Party ◽  
Ligand Complex ◽  
Software Suite ◽  
Dynamics Simulations

This tutorial partially copies steps from How to Assign CHARMM Parameters to Desmond-generated System with viparr4 but differs in the parametrization steps. You can use the Schrödinger software suite to prepare systems for molecular dynamics simulations, however, only the OPLS _2005 and OPLS4 force fields can be automatically assigned. This tutorial will show you how to use Desmond with third-party force fields like AMBER, using the Viparr utility from D.E. Shaw Research. You will prepare a protein-ligand complex, generate custom AMBER parameters for the ligand, and use the Viparr utility to convert the generated AMBER parameters into a viparr-formatted template, that can be used for simulations. You can find the input files for this tutorial here:

scholarly journals Towards exact molecular dynamics simulations with machine-learned force fields

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefan Chmiela ◽  
Huziel E. Sauceda ◽  
Klaus-Robert Müller ◽  
Alexandre Tkatchenko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Dynamics Simulations
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