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

[Alessandro Casoni]

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.
>>
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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