[gmx-users] creating index for first hydration layer water molecules

[Justin Lemkul]

On 6/10/15 2:20 AM, Sahithya S Iyer wrote:
> Thanks for the reply Justin.
>
> I have tried the following:
> g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc
> cfrac.xvg -oi index.dat -select '"Nearby water" resname SOL and within 0.35
> of group Protein'
>

Note that with trajectories you will generate an index file with one group per 
frame, so you have to do the analysis on a per-frame basis, not automatically 
like other tools with fixed index groups.

> But there is a syntax error. Could you please tell me where i could be
> going wrong..
>

Something like -select 'same residue as name OW and within 0.35 of group 
Protein' should do the trick.

-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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