>From my limited experience, ...Also, VMD makes this easier. I learned the hard way to center on a molecule when making the initial box in editconf. Otherwise varied combinations of the -mol, -pbc , -nojump -center options usually work, but never consitent at least for me. Still, if its 4 small molecules it might not make a difference if the other 3 keep moving out of the box.
The only differences I noticed in analyzing these was with distances, and geometric math functions, in which case you would have to analyze each moleucle centered in the .trj (ie 3-4 different centered versions of the same initial .trj) seperat. All the energy and force values were independent of this though. Good luck Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 29 Mar 2012 06:55:06 +0000 > Von: "Rausch, Felix" <frau...@ipb-halle.de> > An: \'Discussion list for GROMACS users\' <gmx-users@gromacs.org> > Betreff: AW: [gmx-users] About movie in GROMACS > Hi. > > Take a look at the "-center" flag of trjconv. Together with "-pbc" (and > maybe also "-ur") it should be possible to center your molecules of interest > in the middle of the simulation cell. > > > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > Im Auftrag von rama david > Gesendet: Donnerstag, 29. März 2012 07:18 > An: Discussion list for GROMACS users > Betreff: [gmx-users] About movie in GROMACS > > HI Gromacs Friends, > I complete one simulation for 4 different molecule placed > apart > in box of dimension 4 4 4 .. > when I used the trajectory I saw the one molecule interact with each other > but they are > getting broken because of box..(Some part protruding from other side). > To see movie I used the command > 1. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc nojump -dt 10 > The molecules moving apart without any interaction > > 2. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc whole -dt 10 > The molecules are interacting in cell .. > but because of periodic cell , near the cell boundary the molecule > interaction get remove and molecules come in cell from other side.. > ( I know it is because of periodic boundary condition ..one goes from > right > hand side come in cell through left hand side ) > > To see the four molecule interacting each other near also cell boundary , > what command > I have to use ??? -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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
