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

Olga Ivchenko olga.ivchenko at gmail.com
Fri Feb 25 11:35:00 CET 2011

```Regarding my previous question. I performed 2 simulations (minimization,
NVT, NPT, and that 10ns production run), one with 300K and another with
309K. Fir each temperature I calculated how many contacts has my molecule
with water within a certain distance. But the number of contacts at
different temperatures is the same. It differs on 0.1. I think it has
something to do with pressure. I would really like to be able to perform
simulations that I could get correct different value of number of contacts
versus temperature.

best,
Olga

2011/2/23 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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
>>
>>
>>    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).
>>
>>                                  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>>
>>                                  <mailto: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!
>>        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>>
>>                                  <mailto: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>>>.
>>
>>
>> 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>
>>        <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>>
>>                      <mailto: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>>
>>                      <mailto: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>>>.
>>
>>        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>>.
>>
>>
>>
>>    --     ========================================
>>
>>    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>.
>>
>>
>>
> --
> ========================================
>
> 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.