Thanks lot. Happy Thanksgiving!. -Xianghong Qi On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni < [EMAIL PROTECTED]> wrote:
> Tsjerk Wassenaar ha scritto: > >> Hi, >> >> Can't help you with VMD, but I do have a script to take care of this in >> Pymol. >> >> Cheers, >> >> Tsjerk >> >> On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: >> >> >>> Dear all: >>> >>> I am trying to show the dodecahedron box only in vmd since my simulation >>> box >>> is dodecahedron. If I include water, I can see the box is dodecahedron. >>> But >>> I want to get rid off all of water, then my box will not appear there. >>> How >>> can I keep the dodecahedron box boundaries and solute only? Looks like >>> only >>> the rectangular box boundaries can be drawn in VMD. >>> Does anyone has some suggestions? Appreciate your great help. >>> Happy Thanksgiving. >>> -Xianghong Qi >>> >>> -- >>> Some people make the world more special just by being in it. >>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.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 >>> >>> >>> >> >> >> >> > Hi, > you can try this: > > trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact* > > or > > trjconv -f ?.trr -s ?.tpr -o output.gro *-pbc mol -ur compact* -e 1 > > well...the first converts all your trajectory and the last command extracts > 1 frame in a gro file.. > > good luck > alessandro > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Some people make the world more special just by being in it.
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