Hi, I was doing
gmx trjconv -f nvt.trr -s em.gro -pbc nojump -e 100 -dt 100 -o test.gro I verify that em.gro is intact. nvt.trr is the output of a simulation whose .tpr file was created by a broken molecule. In any case, -pbc mol with the .tpr file works. Best, Irem > On Feb 1, 2017, at 4:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 2/1/17 3:18 PM, Irem Altan wrote: >> Hi, >> >> For this I tried to do use the unfragmented configuration with the -s flag >> to trjconv when generating the trajectory. This results in a properly >> fragmented molecule, except for a single ILE residue. 3 atoms of this >> residue somehow remain displaced by the box size, while the other atoms of >> the same residue are correctly placed onto the protein. Is this a bug? If >> so, is there any way to circumvent it? (I use 5.1.2) >> > > Without an exact sequence of commands, it's impossible to tell what may have > happened. It is extremely doubtful that trjconv has a bug in simple PBC > routines. > > Reconstructing "broken" molecules should be trivial with trjconv -pbc mol and > a .tpr file passed to -s. > > -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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__mackerell.umaryland.edu_-7Ejalemkul&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=6IwSx9Vp0pz6rDxSY06ktYRiIcvbBCLoP9WaHXZuIhI&e= > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=BfsK71HmIphEaDylHmsmDUH2YP_HNHq29W6vnFqAzKk&e= > before posting! > > * Can't post? Read > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=PHH9uKNUxxZvrwMgeYj0Y90ziG7-S-9kieQu_Y4Kdqk&e= > > * For (un)subscribe requests visit > https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=11xfB38N1LYxHT_mAh2ohF-ThWQUO5iIbnlyemIJ_oA&s=HiotTo0K1_6zUzFVgnbc8i37mXAg6DbHNfBNjoY0AT8&e= > 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.
