Dear Jenny, You can do this directly in VMD, using the Periodic tab under Graphics->Representations.
Ran Jennifer Williams wrote: > > > Hello, > > I am trying to find a way around a visualisation problem I am having > in VMD. Some of my molecules go over periodic boundary conditions > meaning that bonds sometimes appear missing when looking at movies (I > am trying to fix this using wrap, unwrap and join in VMD but as yet no > luck). > > I was wondering if there is a way in gromacs to multiply the number of > unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the > new unit cell to be 2x2x2. This would mean the section of the > structure I want to zoom in doesn't go over the pbc. > > For the confout.gro file I have done this using > > genconf -nbox 2 2 2 -f confout.gro -o confbig.out > > and this enables me to at least see a static image where all bonds are > present. > > but in order to view a movie, I need to carry out something similar on > the traj.xtc file. I have seen that with trjconv there is the option > > -box Size for new cubic box > > but my unit cell is not cubic, it is a parallelepiped. The cell > dimensions are : > > 4.64210 3.77847 1.89596 0.00000 0.00000 -2.18150 0.00000 > 0.00000 0.00000 > > I tried using this anyway with the following command: > > trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc > > but the resulting .xtc file wouldn't load into VMD so I assume that > the .xtc file and the .gro file didn't match. > > Any ideas?, > > Thanks > > Jenny > > > > > > > > --The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > --gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
