Re: [gmx-users] How to save trajectories of our interest into vmd
On 10/27/14 1:25 AM, Seera Suryanarayana wrote: Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. If you're having problems with VMD, they have a mailing list that might suit your question better. If the question relates to how one views or analyzes only a subset of a trajectory, it's rather simple. Gromacs tools make use of the -b and -e options, to allow you to -b(egin) and -e(nd) your analysis at any time frame in the trajectory. If you want to visualize only a short segment of the trajectory, use trjconv -b and -e (using time in ps, not frame number) to write out a new trajectory for visualization. -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.
[gmx-users] How to save trajectories of our interest into vmd
Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- 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.
Re: [gmx-users] How to save trajectories of our interest into vmd
Dear Suryanarayana, Try this, I hope it will help g_rmsf -f file.trr -s file.tpr -res -b 150 -e 160 -ox Required_frame.pdb On Mon, Oct 27, 2014 at 10:55 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- 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. -- 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.
