[gmx-users] Re: how to show dodecahedron box in VMD
xianghong001 at gmail.com
Wed Nov 26 14:58:51 CET 2008
Thanks lot. Happy Thanksgiving!.
On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni <
alessandro.casoni at unimi.it> wrote:
> Tsjerk Wassenaar ha scritto:
>> Can't help you with VMD, but I do have a script to take care of this in
>> 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
>>> is dodecahedron. If I include water, I can see the box is dodecahedron.
>>> I want to get rid off all of water, then my box will not appear there.
>>> can I keep the dodecahedron box boundaries and solute only? Looks like
>>> 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.
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> 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
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