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

[Olga Ivchenko]

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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