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

[Mark Abraham]

Hi,

Which GROMACS tools documentation did you check to see whether it can be
done already? :-) I don't know the answer, but that's where to start!

Mark

On Thu., 28 Feb. 2019, 10:43 Mahsa, <ebadi.mahsa at gmail.com> wrote:

> Thank you very much for your comments!
>
> How would it be possible to get probability vs. number of contacts or
> probability vs coordination number averaged across the simulations? Can it
> be done directly with Gromacs tools or I need some scripts for that?
>
> Best regards,
> Mahsa
>
> On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > --
> > ==================================================
> >
> > 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
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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