Thanks. On Wed, Aug 8, 2018 at 10:16 Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 8/7/18 8:51 AM, Alex wrote: > > Thanks. > > > > On Tue, Aug 7, 2018 at 8:30 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 8/7/18 8:23 AM, Alex wrote: > >>> Dear all, > >>> In the simulation of a system in which there is slab, I did not use > >>> "periodic-molecules > >>> = yes" unfortunately, hence I can not make a good movie out of the > >> This is not some magic setting that will make nice movies. Note that a > >> "periodic molecule" is different from just normal PBC. Periodic > >> molecules are "infinite" molecules like sheets, nanotubes, etc. that > >> have bonds between central image atoms and periodic copies of atoms. If > >> you needed such a setting and did not use it, likely your simulation > >> would have collapsed. > > No, the simulation did not blow up and worked nicely. As far as I > > understood and in general the periodic-molecule = yes should be used > when a > > surface is connected to it's image in the neighbouring cell, mine is > silica > > slab, and if the the slab is defined only by non-bonded interaction like > > most of the metallic slab the periodic molecule = NO should work finely > in > > spite of being infinite. > > Correct. "Periodic molecules" only matter for bonded interactions. > > > > >>> trajectory using VMD, the slab move during the movie. The simulation is > >>> around 300 ns and I do not want to just waste the CPU time, so, I > wonder > >> if > >>> there is still any solution for that to make a good movie out of that > >>> trajectory? > >> Many of the normal trjconv routines could likely help here. Accounting > >> for PBC effects like these is a standard first step in post-processing > >> any trajectory. > >> Actually what I see is the result of two below comments applied over the > >> initial trajectory: > >> > > gmx_mpi trjconv -f prd.xtc -s eql1.gro -o nojump-skip-30-prd.xtc -center > > -pbc nojump -n input/index.ndx -tu ns -skip 30 < choice : salb, system > > gmx_mpi trjconv -f nojump-skip-30-prd.xtc -s prd.tpr -o > > nopbc-nojump-skip-30-prd.xtc -center -pbc whole -ur compact -n > > input/index.ndx -tu ns < choice : salb, system > > If the surface appears to be shifting laterally, then a translational > fit is probably what you want. Do you know please any command for that by heart? Or if gromacs has one for that? > The surface first shift laterally in the very early steps of the trajectory, there are also some Up-Down movement in some frames. Thank you. Regards, Alex > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.