[gmx-users] Re: trjconv for pbc

[Justin Lemkul]

On 11/3/13 7:12 AM, rankinb wrote:
> That last procedure works.  I really appreciate your help.  The only other
> question I have is related to the selection process.  Is there a way to
> select the oxygen atoms of water within a certain distance of a molecule, as
> well as the corresponding hydrogen atoms on the water molecule?  Right now,
> I am able to select hydrogen atoms and oxygen atoms that are within a
> certain distance, but I would like to only select whole water molecules
> whose oxygen atoms are within a cutoff.
>

Start your selection string with "same residue as" and it will select the whole 
residue for any atom that satisfies the selection criteria.

-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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