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

[Olga Ivchenko]

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?

best,
Olga

2011/2/21 Justin A. Lemkul <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>>
>>
>>
>>    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
>
> ========================================
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