Thanks. It's exactly what you said.
ePBC = no On Thu, Mar 13, 2008 at 6:44 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > Editing mdout.mdp will not affect the parameters in your .tpr, and > therefore your simulation, I'm fairly sure. It's just a report of what > you've specified, with all the defaults. > Add the pbc=whatever line into your INPUT mdp to fix this. > > ----- Original Message ---- > From: Liu Shiyong <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, March 13, 2008 11:39:46 PM > Subject: [gmx-users] How to change the default value for pbc ? > > Hi, > > I generated mdout.mdp > > by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o > ${file}.input.tpr . > > The pbc in mdout.mdp is like: > > ; Periodic boundary conditions: xyz (default), no (vacuum) > ; or full (infinite systems only) > pbc = xyz > > It seems that grompp doesnot give an option to change the pbc value. > > I didnot find an easy way to change the pbc value . The only way I found > is to edit the mdout.mdp directly. > > Best > > -- > Shiyong Liu > Research Assistant > center for bioinformatics in the university of kansas > Lab: (785)864-1962 > Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) > Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu> > Lab: http://vakser.bioinformatics.ku.edu/people > Phone: (785) 864-1962 > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > > > ------------------------------ > Never miss a thing. Make Yahoo your > homepage.<http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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