[gmx-users] "wrong" starting structure

Xavier Periole x.periole at chem.rug.nl
Mon Sep 6 12:55:02 CEST 2004

Andrea Carotti wrote:

>Hi gmx-users,
>    I've performed a 18ns MD of a protein. Everything gone fine and now i'm
>analyzing it.
>The starting structure is partially diffused out of the box and when i
>use -pbc nojump the output traj. comes with a chain in a box and the other
>chain in another box so in vmd i have the protein "virtually splitted". I've
>tried also to give as ref. structure a frame with the protein all in a
>single box doing:
>trjconv -f output.trr -o xxx.trr -s right_conf.gro -pbc nojump
>(the so called "reference structure" is that of the option -s?...)
>but nothing changed..what I'm doing wrong?
>Please help me
Perhaps you can try to fit the structure on the ref (-fit option)


   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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