[gmx-users] How to change the default value for pbc ?

Alan Dodd anoddlad at yahoo.com
Fri Mar 14 00:44:57 CET 2008

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 <liushiyong at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, March 13, 2008 11:39:46 PM
Subject: [gmx-users] How to change the default value for pbc ?


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.


Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962

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