thanks again. Guanghong
On Wed, Oct 15, 2008 at 9:10 PM, David van der Spoel <[EMAIL PROTECTED]>wrote: > 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 >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> > > -- > 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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