[gmx-users] editconf and genbox

Shuaib Shahid 0006450S at student.gla.ac.uk
Sat Mar 6 21:16:02 CET 2004


Use the addition "-center 2.0 2.0 2.0" to get the molecules into the center of the box, this goes at the end of the editconf command line. then use genbox but make sure that your box size is at least the size specified at the end of your itp file.

hope this helps

Shuaib Shahid
University of Glasgow
Glasgow, Scotland

-----Original Message-----
From: Mario Orsi <kurtz219 at yahoo.it>
To: gmx-users at gromacs.org
Date: Sat, 6 Mar 2004 18:06:46 +0100 (CET)
Subject: Re: [gmx-users] editconf and genbox

also got the same problem, then I was told to make a " -box x " and then center the molecule "-center x/2". it works fine, at least on gmx 3.2 
"Are u the police?" 
" No ma'am.
- We're musicians" (the blues brothers)

Li Xiaoyi <xiaoyi.li at nat.oru.se> wrote:
Hi all,

I am back.

I tried to put two molecules into a box of water. I used editconf -f -o
-box 4 4 4 -c and then genbox -cp -cs -p -o. But whatever box size I
used, the two molecules are always outside the box. why? What should I


gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.

Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam

More information about the gromacs.org_gmx-users mailing list