[gmx-users] seeking a little help

[Justin Lemkul]

On 11/30/15 12:04 AM, Subho Chakraborty wrote:
> Hi All,
> I am a new student of molecular dynamics. I have started using GROMACS since one month. I have a small question to pose to anyone who is happy to help me.
> I have a small box of 8192 molecules each with 3 atoms. I have frozen the last molecule and run the simulation. I even converted the trr file from binary to .gro and checked that the last molecule indeed stayed in the same place.
> However i want the trr file to print the force on each molecule or each atom - in the x, y and z direction. I even set the "nstfout" in the grompp.mdp file to a reasonable non zero number - 5000.
>
> However the trr file - when converted to .gro - did not show the force. Please can someone tell me what I am doing wrong and how to get GROMACS to save/reveal the force in the trr file.

Extract forces with gmx traj.  There is no way to write forces to a .gro file, 
as .gro can only hold coordinates and (optionally) velocities.

> The second question is this - if I can get it to save the force as part of the snapshot, how can I get it to store the force only on the molecules I specify to be frozen - "the wall" -  (i.e those which have their own .itp file and are specified by the index.ndx file to be held frozen), if this is at all possible - or else I can make do with the forces on all molecules.

gmx traj with that index group.

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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