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.
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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
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