[gmx-users] Questions about GROMACS capabilities

Justin Lemkul jalemkul at vt.edu
Mon Jul 20 14:55:12 CEST 2015

On 7/19/15 7:55 PM, Eric Smoll wrote:
> Hello GROMACS users,
> I have a few questions about what is possible in GROMACS:
> 1.) Is it possible "reset" the velocity of a subset of molecules in a MD
> simulation to an arbitrary, non-thermal distribution? I am particularly
> interested in the situation where all molecules of a certain type are reset
> to a fixed COM speed in a fixed direction.

Not automatically, at least not without code modification.

Otherwise, you'll have to stop your simulation periodically, write velocities to 
a .gro file, then use that .gro file to generate a new .tpr and start a new 
simulation from those velocities.

> 2.) If it is possible to "reset" the velocity of particles in a MD
> simulation, is it possible to do so with a spatial trigger (e.g., all
> molecules that reach the top of the unit cell have their velocity reset to
> a specific speed and direction)?
> 3.) Is it possible to make a gas-liquid system where there are gas-liquid
> interactions but no gas-gas interactions?

Use energygrp_excl.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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