[gmx-users] Re: how to show dodecahedron box in VMD

Alessandro Casoni alessandro.casoni at unimi.it
Wed Nov 26 14:53:43 CET 2008

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 <xianghong001 at gmail.com> 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    gmx-users at gromacs.org
>>  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 gmx-users-request at gromacs.org.
>>  Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
you can try this:

trjconv -f ?.trr -s ?.tpr -o output.trr *-pbc mol -ur compact*


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

More information about the gromacs.org_gmx-users mailing list