[gmx-users] Distance between COM of two groups

[Mark Abraham]

Hi,

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Mark

On Sun, 19 Jun 2016 16:36 Sajjad Kavyani <kavyani.sajjad at gmail.com> wrote:

> Thanks for the reply Justin,
> Actually the pulling process is so simple where the group1 is fixed in one
> side of the box and the group2 on the other side (box center is in the
> middle). And the group2 is moving toward group1 (in a straight z
> direction). It is so logical that the distance between them must start from
> a maximum value  and decreases over time but the output distance from "gmx
> distance" is a growing value and after some times it decrease slightly!! I
> checked the trajectory with vmd and it shows what I was expected and the
> group2 approach over time to group1 and the distance decreases. It seems
> that everything is correct except the "gmx distance" output.
>
> Actually it seems that the thing that one of the groups is in the negative
> side of the box vector (consider group2 at z = -a and group1 at z = +b),
> the gmx distance tool subtract the "a" from "b" until it passes the zero
> point in the middle of the box and after that the distance decreases vs.
> time!!!
>
> Please find the "gmx distance" output in the attachment.
>
> Cheers
>
> On Sun, Jun 19, 2016 at 3:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 6/18/16 9:40 AM, Sajjad Kavyani wrote:
> >
> >> Dear experts,
> >>
> >> I am puling group2 toward group1 and I want to calculate the distance
> >> between COM of two groups versus time.
> >> For the g_dist it was a straightforward process with the selection menu.
> >> But for the "gmx distance" I used:
> >>
> >> gmx distance  -f test.xtc -s test.tpr -oav -oxyz -n index.ndx
> >> -select 'com of group "group1" plus com of group "group2"'
> >>
> >> But both outputs distances are a growing value over time (!!)
> >> (actually the average value is the same with sqrt(x^2+y^2+z^2)) where
> >> the distance meant to be decrease over time!
> >>
> >> Could you please help me with the commands?
> >>
> >>
> > That's the correct command.  Is there some reason why you think the
> result
> > is wrong?  Are your group definitions correct for the analysis you're
> > trying to perform?
> >
> > -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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