Re: [gmx-users] Number of water molecules around any methyl carbon
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 -- == 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
Re: [gmx-users] Number of water molecules around any methyl carbon
Count the number of O observed near each C singly and compare the four numbers. Mark On Nov 6, 2013 4:57 PM, rankinb rank...@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 -- View this message in context: http://gromacs.5086.x6.nabble.com/Number-of-water-molecules-around-any-methyl-carbon-tp5012297.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
