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

[rankinb]

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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