On 11/19/13 11:13 AM, Asaminew Haile wrote:
Hi Gromacs Users I'm new for gromacs analysis I'm running MD in a 40 ns time interval. I want to strip the water and re-image the molecule. But I found that only if I trjcat all trajectories from the start I can be able to re-image them. Can someone show me how to re-image them independently? Here is what I want for every x in 1000 do echo 1 | trjconv -s md.($x+40).tpr -f md.($x+40).xtc -o strip.($x+40).xtc -pbc nojump # strip water and re-image done
The use of -pbc nojump assumes that the reference frame is suitable for removing jumps. If you have individual .tpr files that correspond to the different trajectories, they may have different reference positions and you won't necessarily get what you want.
The easiest method is (assuming each trajectory is topologically identical and differs only in its coordinates) to create a single reference .tpr file that is suitable for removing jumps.
Most of that information and other useful trjconv help can be found at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.
-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 ================================================== -- 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.
