[gmx-users] Fwd: Probability of number of atomic contacts

Mahsa ebadi.mahsa at gmail.com
Thu Feb 28 15:00:36 CET 2019

Hi Justin,

Could you please comment on my questions in the previous post?

Best regards,

---------- Forwarded message ---------
From: Mahsa <ebadi.mahsa at gmail.com>
Date: Sun, Feb 17, 2019 at 2:36 PM
Subject: Re: [gmx-users] Probability of number of atomic contacts
To: <gmx-users at gromacs.org>

Thank you very much, Justin!

I tried this command:

gmx_seq analyze -f numcont.xvg -dist num_dist.xvg

and I got a histogram. Now the number of contacts between the ion and the
polymer is between 160-180. I just want to be sure if I am doing this
analysis correct. When I use gmx mindist, from the index file I choose a
group of the ion (including 46 ions) and then the polymer group (all
polymer chains in the box).  I think maybe instead of choosing all ions, I
should only select one of them and get the number of contact with the
polymers but then since I have 46 of this ion in the simulation box, can it
be a good representative of the whole system? If not, what else can I do in
this case?

Besides, it is mentioned in the Gromacs manual, that if we use the
-group option
a contact of an atom in another group with multiple atoms in the first
group is counted as one contact instead of as multiple contacts. I want to
count all contact with a polymer chain as 1 contact and check the number of
contacts with different polymer chains so by using -group and having the
ion as the first group and polymer as the second group from the index file,
can I get this?

The last question, can I do the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?

Best regards,

On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:

> On 2/17/19 7:21 AM, Mahsa wrote:
> > Dear Gromacs users,
> >
> > I want to get histograms of the number of polymer-ion contacts average
> > across the simulation. For this I used,
> >
> > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od
> mindist.xvg
> > -on numcont.xvg -or mindistres.xvg -group
> >
> > and from the index file, I chose the ion first and then the polymer
> group.
> > The generated file numcont.xvg which is more related to what I am looking
> > for, gives number of contacts vs time. How can I get the information
> which
> > I look for from this analysis?
> Post-process with gmx analyze -dist
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
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> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
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