From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Mar 09 2006 - 13:26:53 CST
Maybe you should take a look at the "ptraj" program (which is also a
free standalone program apart from being distributed with AMBER -
http://www.chpc.utah.edu/~cheatham/software.html)...
Otherwise, you can easily covert your dcd trajectory into a sequence of
PDB files free of waters with VMD ....
vlad
griadi_at_utalca.cl wrote:
>I wouldn't know how to edit the .dcd file before loading it to VMD but maybe, if
>you load the .dcd in two parts (e.g. first frame and the rest of the .dcd, using
>catdcd) then you might load the whole system frame, take the waters away in
>graphics representations and just load the rest of the .dcd (without waters).
>
>Gonzalo.
>
>Mensaje citado por lily jin <lily1907_at_yahoo.com>:
>
>
>
>>I need the waterbox to do simulation. But when I show the result in VMD, the
>>waterbox is not necessary, which takes a lot of memory. Is it possible to do
>>simulation with waterbox and remove it from the trajectory before displaying
>>in VMD?
>>
>> Thanks!
>>
>>
>>Lily
>>
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>
>
>
>
>-------------------------------------------------
>Este mensaje fue enviado por: http://webmail.utalca.cl
>
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>
-- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Schloss-Wolfsbrunnenweg 33 69118 Heidelberg, Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/
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