[gmx-users] Number of water molecules around any methyl carbon

[Justin Lemkul]

On 11/6/13 10:55 AM, rankinb wrote:
> Hi all,
>
> I would  like to calculate the number of water molecules around any of the
> methyl carbon atoms of tert-butyl alcohol.  Currently, I have defined an
> index group containing all three of the methyl carbon atoms and used
> trjorder -nshell to calculate the number of oxygen atoms within a specified
> cutoff distance of this index group.  What I am trying to figure out is
> whether this method results in the number of oxygen atoms around any single
> methyl carbon or all methyl carbon atoms.  Does anyone have any insights
> regarding this problem?  If the described method does not calculate the
> number of oxygen atoms around all of the methyl carbon atoms, is there a way
> to do so, without overcounting?
>

It should account for all of the methyl groups simultaneously, but you'd have to 
go into the code to see if it is doing the searching based on all of the atoms 
or just the group's center of mass.  In the latter case, you'd be potentially 
under-counting the number of waters.

Integrating an RDF would be a more conventional approach.

-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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