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

[gozde ergin]

Thanks Justin !
> On 12 Jun 2017, at 14:01, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
> 
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