Thanks.<br><br>It's exactly what you said.<br><br><br> ePBC = no<br><br><br><div class="gmail_quote">On Thu, Mar 13, 2008 at 6:44 PM, Alan Dodd <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><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;"><div><div></div><div class="Wj3C7c">----- Original Message ----<br>From: Liu Shiyong <<a href="mailto:liushiyong@gmail.com" target="_blank">liushiyong@gmail.com</a>><br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><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" rel="nofollow" target="_blank">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu" rel="nofollow" target="_blank">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu" rel="nofollow" target="_blank">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/%7Esyliu" rel="nofollow" target="_blank">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people" rel="nofollow" target="_blank">http://vakser.bioinformatics.ku.edu/people</a><br>
Phone: (785) 864-1962
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><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">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone: (785) 864-1962