[gmx-users] Visualization Problem

Itamar Kass ikass at uq.edu.au
Tue May 8 05:04:19 CEST 2007

Shalom George

Maybe your nanotube 'jump' over the PBC?

Try 'trjconv -pbc whole ...'


George Abadir wrote:
> Hi,
>     I finished a simulation of a carbon nanotube in water. I made a 
> movie of the simulation using 'trjconv' to view with Pymol. The problem 
> is that starting from the third frame it messes the carbon nanotube 
> bonds. I changed the start time and again in the third frames it messed 
> things up. I output each frame in a different file using the '-sep' 
> option and it could read each one successfuly, so I think the problem is 
> in reading them in sequence. Can anyone help with that?
>    Thank you very much,
> Regards,
> George
> _______________________________________________
> 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

"Prediction is very difficult, especially about the future" - Niels Bohr

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Molecular Dynamics Group
| School of Molecular and Microbial Sciences (SMMS)
| Chemistry Building (#68)
| The University of Queensland
| St. Lucia Campus, Brisbane, QLD 4067
| Australia
| Tel: +61 7 3365 9922
| Fax: +61 7 3365 3872
| E-mail: ikass at uq.edu.au
| Web page: http://www.uq.edu.au/~uqikass/
| Personal web page: http://thekassfamily.blogspot.com/

Unless stated otherwise, this e-mail represents only the views of the 
Sender and not the views of The University of Queensland

More information about the gromacs.org_gmx-users mailing list