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

Olga Ivchenko olga.ivchenko at gmail.com
Wed Feb 23 14:14:38 CET 2011

```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.

best,
Olga

2011/2/23 Justin A. Lemkul <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>>
>>
>>
>>
>>    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>>>
>>
>>
>>           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>>>
>>
>>
>>
>>               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
>>
>>                           --                     gmx-users mailing list
>>           gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>                           <mailto:gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>>
>>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>                           Please search the archive at
>>
>> http://www.gromacs.org/Support/Mailing_Lists/Search
>>                           before posting!
>>                           Please don't post (un)subscribe requests to the
>>                           list. Use the
>>                           www interface or send it to
>>                           gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>                           <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>
>>                           Can't post? Read
>>                           http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>
>>               --         ========================================
>>
>>               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
>>
>>               ========================================
>>
>>               --         gmx-users mailing list
>> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>               <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org
>> >>
>>
>>
>>               http://lists.gromacs.org/mailman/listinfo/gmx-users
>>               Please search the archive at
>>               http://www.gromacs.org/Support/Mailing_Lists/Search
>>        before posting!
>>               Please don't post (un)subscribe requests to the list. Use
>> the
>>               www interface or send it to gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>               <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>
>>               Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>    --     ========================================
>>
>>    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
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110223/61f060d3/attachment.html>
```