scholarly journals Evaluation of all-atom force fields in viral capsid simulations and properties

RSC Advances ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 216-220
Author(s):  
Ruijie D. Teo ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Viral Capsid ◽  
Viral Capsids ◽  
Dynamics Simulations

We investigate six AMBER and CHARMM force fields for molecular dynamics simulations of viral capsids. Out of the force fields studied, we recommend CHARMM36m and CHARMM36 for future use.

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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