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

[Mahboobe Sadr]

  Does it mean,  i can't do that automatically??



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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