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

[Alan Dodd]

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 ?

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: 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


-----Inline Attachment Follows-----

_______________________________________________
gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080313/ccfc5485/attachment.html>