[gmx-users] Distance between COM of two groups

[Sajjad Kavyani]

I uploaded the output file to google drive. Please find the link below:
https://drive.google.com/open?id=0B8rMZ-61IzIWYmE4Z2NPTlpjU2s

On Sun, Jun 19, 2016 at 8:56 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The list cannot accept attachments. Please upload the file to a sharing
> service and share the link.
>
> 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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