[gmx-users] Giving an initial velocity to a group of atoms

Justin Lemkul jalemkul at vt.edu
Mon May 11 22:38:53 CEST 2015

On 5/11/15 11:03 AM, Jashimuddin Ashraf wrote:
> Thanks again for your reply Dr. Lemkul.
> I was also expecting a disaster because I gave an unrealistic starting
> velocity of the structure. But the simulation was running fine. I tried
> using the gmxdump and found that the velocities I am getting are not the
> velocities I've given to the atoms.
> In your reply you were kind to reply that "You need to use proper formatting
> "
> I am following the format in the lilnk -
> http://chembytes.wikidot.com/g-grofile
> what I did was I just added 3 extra columns to my .gro file manually after
> getting .gro file from editconf. What might be my problem?

Without access to all of your files, there's no way to know.  If you want to 
upload a tarball of your .gro, topology, and .mdp file, that will help.



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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