thank you very much. I do it by the trjconv. A new small problem. I want get a picture that the protein is in the water box. Now I must get it by two steps. trjconv ....-pbc whole ... and then trjconv ...-pbc atom -ur compact
can I do it in one step? thinks Guanghong On Wed, Oct 15, 2008 at 8:29 PM, Justin A. Lemkul <[EMAIL PROTECTED]> 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. > > -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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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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