[gmx-users] center of mass motion

[leafyoung81-group at yahoo.com]

use trjconv -center tric -f in.xtc -o out.xtc

Yang Ye
Nanyang Technolgoical University, Singapore

----- Original Message ----
From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, January 04, 2006 7:16:40 PM
Subject: Re: [gmx-users] center of mass motion

hi

On Wednesday 04 January 2006 11:22, herbst at fhi-berlin.mpg.de wrote:
> Hi all,
>
> my protein is jumping out of the box during the simulation. I tried to
> center it in the box using trjconv -pbc inbox -center, but when I look at
> the new trajectory, it is still leaving the box and I can't watch it.
> Am I doing something wrong ?
Take a reference strucuture which is inside the box, normally the minimized em 
or pr file. ( trjconv -s file. ...)


> And how can I constrain the center of mass motion in the simulation ?



>
> Thanks,
> Anna
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.