Experiment vs Force Fields:  DNA Conformation from Molecular Dynamics Simulations

1997 ◽  
Vol 101 (38) ◽  
pp. 7361-7363 ◽  
Author(s):  
Michael Feig ◽  
B. Montgomery Pettitt
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Dna Conformation ◽  
Dynamics Simulations

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

Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields

2018 ◽  
Vol 20 (13) ◽  
pp. 8676-8684 ◽  
Author(s):  
Yanhua Ouyang ◽  
Likun Zhao ◽  
Zhuqing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Structural Ensembles ◽  
Dynamics Simulations

The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.

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