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

[Justin A. Lemkul]

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>>
> 
>     Thank you very much.
>     best,
>     Olga
> 
>     2011/2/21 Justin A. Lemkul <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> | (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

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