# [gmx-users] how many contacts has a certain atom at MD

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 23 14:21:39 CET 2011

```
Olga Ivchenko wrote:
> Yes, I want to plot number of contacts agains tempreture. But in
> thermodynamics when temperature changes the pressure changes or the
> volume. But in my system volume and pressure is the same at different
> tempretures. Just I wanted ti be sure if it is ok to do like this even
> if the pressure is the same at different tempretures.
>

I guess this all depends on how "different" your temperatures are.  If the
pressures do not change substantially, then there is no problem, since the
system density is reasonably similar.

-Justin

> best,
> Olga
>
> 2011/2/23 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     Olga Ivchenko wrote:
>
>         If I am using g_mindist to calculate the number of contacts at
>         different tempretures of the system. I am thinking if it will
>         make sense because the system has a periodic boundary conditions
>         and the pressure at each tempreture is defined manually and is
>         the same. The only parameter in the script which should be
>         different at different tempretures is pressure. Please could you
>         advice me on this?
>
>
>     So you want to plot contacts as a function of temperature?  I don't
>     see any problem with doing that.  On what do you need advice?
>
>     -Justin
>
>         best,
>         Olga
>
>         2011/2/21 Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>>>
>
>
>
>            Olga Ivchenko wrote:
>
>                So I used mindist for a certain group of molecules which is
>                surrounded by water. I got plot number of contacts versuc
>                sumulation time. According to what I see in a distance  <
>         0.6nm
>                at certain frame there are on average 150 contacts.
>
>                Actually how the programm calculates the number of
>         contacts, if
>                someone knows what is a creteria that a certain contact
>         is formed?
>                Is is a certain distance.
>
>
>            Exactly as the title of the output says, a contact exists if
>         any two
>            atoms of the chosen index groups are within 0.6 nm.  You can
>         change
>            the distance with g_mindist -d.
>
>            -Justin
>
>                best,
>                Olga
>
>                2011/2/21 Olga Ivchenko <olga.ivchenko at gmail.com
>         <mailto:olga.ivchenko at gmail.com>
>                <mailto:olga.ivchenko at gmail.com
>         <mailto:olga.ivchenko at gmail.com>>
>         <mailto:olga.ivchenko at gmail.com <mailto:olga.ivchenko at gmail.com>
>
>                <mailto:olga.ivchenko at gmail.com
>         <mailto:olga.ivchenko at gmail.com>>>>
>
>
>                   Thank you very much.
>                   best,
>                   Olga
>
>                   2011/2/21 Justin A. Lemkul <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>
>
>
>                       g_mindist -on (with suitable index groups) should
>         also do
>                the trick.
>
>                       -Justin
>
>
>                       Erik Marklund wrote:
>
>                           Or g_hbond -contact. Undfortuntely there are
>         still issues
>                           with g_hbond at the moment. Version 4.0.x seem to
>                work better.
>
>                           XAvier Periole skrev 2011-02-21 11.37:
>
>                               g_dist
>                               On Feb 21, 2011, at 11:32 AM, Olga
>         Ivchenko wrote:
>
>                                   Dear Gromacs Users,
>
>                                   I would like to know if there is in
>         gromacs an
>                                   option how to calculate how many
>         contacts has a
>                                   certain atom i(n a molecules of interest)
>                with water
>                                   during the whole MD simulations (or at
>         each
>                step of MD).
>                                   Please could you advice me on this?
>
>                                   best,
>                                   Olga
>
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>                       --         ========================================
>
>                       Justin A. Lemkul
>                       Ph.D. Candidate
>                       ICTAS Doctoral Scholar
>                       MILES-IGERT Trainee
>                       Department of Biochemistry
>                       Virginia Tech
>                       Blacksburg, VA
>                       jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
>         <http://vt.edu> |
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>            --     ========================================
>
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>     --
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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