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

[Sahithya S Iyer]

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'

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

On Tue, Jun 9, 2015 at 5:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/9/15 5:11 AM, Sahithya S Iyer wrote:
>
>> Dear Users,
>>
>> The first hydration layer, to the best of my understanding, is the first
>> minimum in the protein (backbone)-water radial distribution function. How
>> do I create an index for the water molecules in the first hydration layer?
>>
>>
> The hydration layer around a protein includes the full protein, not just
> the backbone.  You can, of course, analyze whatever makes sense to you, but
> the whole protein is typically considered in most experiments, and
> certainly is the case if anyone talks about the "protein hydration layer."
>
> gmx select can do this.  See examples in the help info.
>
> -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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-- 
Sahithya S Iyer