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 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

gmx-users mailing list    gmx-users@gromacs.org
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to