Dear Justin, Thank you very much.
Best regards, Mijiddorj > > On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much for reply. > > My commands > > > > gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump > > gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol -ur compact -n > > ../index.ndx -fit transxy -o md_noPBC.xtc > > > > I got the inconsistent shifts error middle of the trajectory. > > > > Don't use -pbc and -fit simultaneously. Do -pbc mol then do whatever > fitting > you want. Simultaneously trying to re-wrap PBC and apply any sort of > fitting is > incompatible. > > -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].
