[gmx-users] Fwd: Probability of number of atomic contacts
ebadi.mahsa at gmail.com
Thu Feb 28 15:00:36 CET 2019
Could you please comment on my questions in the previous post?
---------- 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
Besides, it is mentioned in the Gromacs manual, that if we use the
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?
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
> > -on numcont.xvg -or mindistres.xvg -group
> > and from the index file, I chose the ion first and then the polymer
> > 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
> > I look for from this analysis?
> Post-process with gmx analyze -dist
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users