[gmx-users] velocity generation in Gromacs 2016

Justin Lemkul jalemkul at vt.edu
Tue Jan 24 16:49:16 CET 2017

On 1/24/17 10:42 AM, Kukol, Andreas wrote:
> Hello,
> I always used to generate velocities for an MD run in the equilibation step by setting
> gen-vel    yes
> in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not set. Does it mean velocities are now generated by default ?
> http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#mdp
> The reason behind my question is, I actually forgot to set it and the MD-simulation seemed to run normally.

The default is to not generate velocities, which has been the default for many 


So your simulation will start out at 0 K and the thermostat will try to bring it 
up to the correct temperature, unless the input coordinate file has velocities 
(e.g. in a .gro file).  You can confirm what happened in the .log file, where 
the initial temperature is printed.



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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