scholarly journals Accurate Calculation of Barnase and SNase Folding Energetics Using Short Molecular Dynamics Simulations and an Atomistic Model of the Unfolded Ensemble: Evaluation of Force Fields and Water Models

2019 ◽  
Vol 59 (10) ◽  
pp. 4350-4360 ◽  
Author(s):  
Juan José Galano-Frutos ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Atomistic Model ◽  
Accurate Calculation ◽  
Water Models ◽  
Dynamics Simulations

Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Sachini P. Kadaoluwa Pathirannahalage ◽  
Nastaran Meftahi ◽  
Aaron Elbourne ◽  
Alessia C. G. Weiss ◽  
Chris F. McConville ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamic Properties ◽  
Systematic Comparison ◽  
Water Models ◽  
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:

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