<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">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.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Add the pbc=whatever line into your INPUT mdp to fix this.<BR><BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Liu Shiyong <liushiyong@gmail.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Thursday, March 13, 2008 11:39:46 PM<BR>Subject: [gmx-users] How to change the default value for pbc ?<BR><BR>Hi,<BR><BR>I generated mdout.mdp <BR><BR>by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o ${file}.input.tpr .<BR><BR>The pbc in mdout.mdp is like:<BR><BR clear=all>; Periodic boundary conditions: xyz (default), no (vacuum)<BR>; or full (infinite systems only)<BR>pbc = xyz<BR><BR>It seems that grompp doesnot give an option to change the pbc value.<BR><BR>I didnot find an easy way to change the pbc value . The only way I found is to edit the mdout.mdp
directly.<BR><BR>Best<BR><BR>-- <BR>Shiyong Liu<BR>Research Assistant<BR>center for bioinformatics in the university of kansas<BR>Lab: (785)864-1962<BR>Email: <A href="mailto:syliu@ku.edu" target=_blank rel=nofollow ymailto="mailto:syliu@ku.edu">syliu@ku.edu</A> (<A href="mailto:shiyongliu@ku.edu" target=_blank rel=nofollow ymailto="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</A> or <A href="mailto:liushiyong@ku.edu" target=_blank rel=nofollow ymailto="mailto:liushiyong@ku.edu">liushiyong@ku.edu</A>)<BR>Homepage: <A href="http://www.people.ku.edu/~syliu" target=_blank rel=nofollow>http://www.people.ku.edu/~syliu</A><BR>Lab: <A href="http://vakser.bioinformatics.ku.edu/people" target=_blank rel=nofollow>http://vakser.bioinformatics.ku.edu/people</A><BR>Phone: (785) 864-1962<!-- kill -->
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