[gmx-users] g_select

[SEMRAN İPEK]

Dear justin;

As usual, it is of your kindness to explain extensively. I will give it try
and let you know.

Best regards;

semran


2013/11/18 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> gromacs.org_gmx-users mailing list    gromacs.org_gmx-users@
> maillist.sys.kth.se
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists