[gmx-users] trjconv

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jul 14 14:54:53 CEST 2004

I think you need to have an reference conformation where the complex
is whole, otherwise trjconv -pbc won't know how to reposition the
molecules. You can read in a different reference conformation with
the -s option, which might help. Or try the -cluster option. But I am
not an expert....


---- Message from Kay Gottschalk <kay.gottschalk at weizmann.ac.il> at
2004-07-14 15:23:02 ------
>I have a protein complex at the edge of the box, so that one part of 
>the complex is wrapped (in the initial conformation after editconf). 
>For pretty pictures (movies) I'd like to have the complex as a
>Somehow trjconv -pbc whole -center doesn't seem to do the trick. Any 
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