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 <[email protected]>
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
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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