[gmx-users] find hbond between different groups during simulation

[Justin Lemkul]

On 1/21/16 1:11 AM, Mahboobe Sadr wrote:
>    Does it mean,  i can't do that automatically??
>

It's simple to dump out each frame and perform the analysis in a scripted loop. 
  That's about as automatic as anything gets.  Precompiled programs don't exist 
for every possible situation you might dream up.

-Justin

>
>
> On Thursday, January 21, 2016, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 1/20/16 4:08 AM, Mahboobe Sadr wrote:
>>>
>>> Dear all,
>>>
>>> I want to find hydrogen bonds between waters and The protein. since in
> each
>>> frame I selected some specifc waters, I want to find hydrogen bonds
> during
>>> simulation for different waters(which are in the pore of the protein) and
>>> the protein.
>>>    as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
>>> couldn't find the hbond i want.
>>>
>>
>> Use gmx select to get per-frame index groups that satisfy the selection
> criteria, then run the analysis frame by frame.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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