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

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 15 15:10:10 CEST 2008

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
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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