On 10/17/15 5:32 AM, Deva Priya wrote:
Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or should I use the
This is correct.
gmx rdf -yescom
Boolean options are never prefixed with "yes" so you would have gotten an obvious fatal error here.
In each case I would specify the group that contains SO3 atoms twice for the rdf calculation.
Yes. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
