[gmx-users] extract the coordinate by using traj command for sphere system

[Justin Lemkul]

On 6/12/17 4:36 AM, gozde ergin wrote:
> Dear all,
> 
> In order to calculate the osmotic pressure I would like to extract the coordinate of my atoms by using g_traj command.
> 
> Before my box was cubic and by using
> 
> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox -noy
> 
> I was getting coordinate of all of my atoms in the system. So this was working fine.
> 
> However now my system is sphere and I again want to extract the coordinate file of all my atom. However if I use:
> 
> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -com
> 
> I only get the coordinate X,Y and Z component not all atoms coordinates.
> 

Because you're doing something totally different here than in the command above. 
  Here, you're asking for (x,y,z) coordinates of the COM of the selection.

> Do you have any hint how to extract the atoms coordinate files in gromacs for sphere system?
> 

It's no different than any system.  Use gmx traj as you did in the first 
command, with a proper selection.  Geometry of the system is irrelevant.

-Justin

-- 
==================================================

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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