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

Justin Lemkul jalemkul at vt.edu
Thu Feb 28 19:17:26 CET 2019

On 2/28/19 8:59 AM, Mahsa wrote:
> Hi Justin,
> Could you please comment on my questions in the previous post?
> Best regards,
> Mahsa
> ---------- 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?

I don't see any point in doing per-ion analysis. You already have the 
answer you want with respect to contacts between the two species. 
Choosing one ion isn't necessarily going to be representative, either.

> 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?

This option is primarily used to avoid over-counting, e.g. the 
interaction between an ion and carboxylate oxygens will not be counted 
as two contact if each ion-oxygen distance satisfies the criterion; it's 
just one.

> 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?

You can calculate coordination number by integrating an RDF.



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


More information about the gromacs.org_gmx-users mailing list