[gmx-users] PBC problem

Xavier Periole x.periole at chem.rug.nl
Thu Jul 8 17:17:24 CEST 2004

Andrea Carotti wrote:

>Hi gmx-ers,
>    I'm trying to visualize with vmd my trajectory (only the protein,
>without water). I think I'm having problem with the pbc option of trjconv.
>During the simulation (in vmd) a chain of my protein jumping. It's for sure
>that this appens when that portion of protein goes out from the box
>(octhaedron type).
>I've tried -pbc nojump -center (using the protein group) and -pbc
>whole -center -fit progressive but without success.
>Please someone could  suggest me something to check or to try
>gmx-users mailing list
>gmx-users at gromacs.org
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A simple solution is to use
trjconv -f traj.xtc -fit -o traj-fitted.xtc

if the protein is centered in your initial conf you get what you want.


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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