On 5/3/17 2:33 AM, Nikhil Maroli wrote:
Dear all, I wanted to calculate the position of the water molecules during the simulation time. This is for understanding the movements of water molecules through a channel protein. How I can get this information using gromacs. I'm looking for something like this in Fig (b) https://drive.google.com/file/d/0BxaQk_pcR9viS3I3NDlKSURuUGs/view?usp=sharing
This can be done with gmx traj -ox -z. Choose which waters to monitor via gmx select or some other suitable criteria.
-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 [email protected] | (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 [email protected].
