scholarly journals Molecular dynamics simulations on DNA flexibility: a comparative study of Amber bsc1 and bsc0 force fields

2018 ◽  
Vol 67 (10) ◽  
pp. 108701
Author(s):  
Xiong Kai-Xin ◽  
Xi Kun ◽  
Bao Lei ◽  
Zhang Zhong-Liang ◽  
Tan Zhi-Jie
Keyword(s):  
Molecular Dynamics ◽  
Comparative Study ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Dna Flexibility ◽  
Dynamics Simulations

A comparative study of two classical force fields on statics and dynamics of [EMIM][BF4] investigated via molecular dynamics simulations

2008 ◽  
Vol 129 (22) ◽  
pp. 224501 ◽  
Author(s):  
Florian Dommert ◽  
Jochen Schmidt ◽  
Baofu Qiao ◽  
Yuanyuan Zhao ◽  
Christian Krekeler ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Comparative Study ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Statics And Dynamics ◽  
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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