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

[Olga Ivchenko]

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.

best,
Olga

2011/2/21 Olga Ivchenko <olga.ivchenko at gmail.com>

> Thank you very much.
> best,
> Olga
>
> 2011/2/21 Justin A. Lemkul <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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
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