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

[Justin Lemkul]

On 6/12/17 7:59 AM, gozde ergin wrote:
> But I need to understand if atoms go beyond the wall (flat-bottom restraint).
> 
> In order to understant that I need to know their coordinate with respect to radius.
> 
> Do you think I should use the basic math here :  r = (x^2 + y^2 + z^2)^(1/2) ?
> 

Yes, you still need to consider the individual (x,y,z) of each restrained atom. 
A COM selection does you no good.  You'll have to determine the displacement of 
each atom from the reference position of the restraint potential.

-Justin

> 
>> On 12 Jun 2017, at 13:55, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> 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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-- 
==================================================

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

==================================================