[gmx-users] editconf and genbox

[Shuaib Shahid]

Hi,

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
www.gla.ac.uk 

-----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
do?

Thanks,
Xiaoyi

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