2011/1/7 Justin A. Lemkul <jalem...@vt.edu> > > > Qin Qiao wrote: > >> Dear all, >> >> I came across a problem when I want to make the REMD trajectories >> continuous. >> >> What I did: >> >> 1. 'demux.pl <http://demux.pl> REMD_0.log' --to get the >> 'replica_index.xvg' >> >> 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' >> >> It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I >> found it's still discontinuous.. with big jumps about 0.5nm..! Could you >> help me to figure out what's wrong? Thanks a lot. >> >> > Have you properly accounted for periodicity effects? > > -Justin >
It's the same after I remove periodicity by trjconv -pbc mol -ur compact ... > Best, >> >> Qin >> >> -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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