Molecular dynamics simulations of melting and sintering of Si nanoparticles: a comparison of different force fields and computational models

2018 ◽  
Vol 20 (3) ◽  
pp. 1707-1715 ◽  
Author(s):  
Luca Sementa ◽  
Giovanni Barcaro ◽  
Susanna Monti ◽  
Vincenzo Carravetta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interaction Potential ◽  
Computational Models ◽  
Silicon Nanoparticles ◽  
Force Fields ◽  
Simulation Procedure ◽  
System Type ◽  
Si Nanoparticles ◽  
Dynamics Simulations

Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential.

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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