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

[Mark Abraham]

Count the number of O observed near each C singly and compare the four
numbers.

Mark
On Nov 6, 2013 4:57 PM, "rankinb" <rankinb at purdue.edu> 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?
>
> Thanks,
> Blake
>
> PhD Candidate
> Purdue University
> Ben-Amotz Lab
>
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