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

[Justin A. Lemkul]

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
> 
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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
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>                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

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