Justin A. Lemkul wrote:
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).
http://www.gromacs.org/pipermail/gmx-users/2008-October/036920.html
And yes, trjconv *does* fix the broken molecules; use trjconv -pbc whole
with your .tpr file.
The officially blessed version is
trjconv -pbc mol [ -ur compact ]
-Justin
thanks
Guanghong
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David van der Spoel, Ph.D., Professor of Biology
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