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

[xianghong qi]

Thanks lot. Happy Thanksgiving!.
-Xianghong Qi

On Wed, Nov 26, 2008 at 8:53 AM, Alessandro Casoni <
alessandro.casoni at unimi.it> 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 <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
>
>
>
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-- 
Some people make the world more special just by being in it.
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