[gmx-users] g_select

[Justin Lemkul]

On 11/15/13 6:49 AM, SEMRAN İPEK wrote:
> Dear gromacs users;
>
> I have been trying to find out the waters close to certain residue. Here is
> my selection dat:
>
> waterO = name "OW";
> close = waterO and within 0.35 of resnr 334;
> close
>
>
> **************************************
> I have been using the command of "g_select -f md_30.xtc -b 30000 -e 30000
>   -s md_30.gro -oi index.dat -sf selection.dat"
>
> Somehow the code sometimes finds the waters within 0.35 nm of residue  and
> sometimes finds the waters too far away from protein (30 nm away .)
>

Does that distance perhaps coincide with a periodic image in which the distance 
criterion is satisfied?

>
>
> Could you please guide me along the process for g_select?
>

Check to make sure all of your criteria make sense.  Write an index group (from 
g_select) that specifies just "resnr 334" to verify that the coordinates are 
being processed and that you don't need something more specific like 'group 
"Protein" and resnr 334.'

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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