[gmx-users] A matter on outputting trajectory of gromacs 4.0

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 15 14:29:36 CEST 2008

G.H. Zuo wrote:
> Dear Gromacs Users
> I download the new gromacs 4.0 and do some tests on protein folding.
> It seem that there is a matter on outputting trajectory in this version.
> When the protein is at the boundary of the box, the mdrun will output the
> protein in some segments.  This matter had never found in the preview
> versions.  And It seem that the program trjconv can't correct this matter.
> Is there someone having ideas about this?

I reported this as well, and it has to do with the new domain decomposition 
scheme (thanks, Tsjerk).


And yes, trjconv *does* fix the broken molecules; use trjconv -pbc whole with 
your .tpr file.


> thanks
> Guanghong
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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