[gmx-users] Problem with box-type after the extension of simulation

Amit Choubey kgp.amit at gmail.com
Thu Nov 19 07:38:14 CET 2009

On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain <sukesh at atc.tcs.com>wrote:

> Dear All,
> I started a protein simulation for 100ps with octahedron box. After
> completion of that run I visualized the protein at the centre of the
> octahedron box by using trjconv.
> Then I have extended the simulation for another 500 ps by using tpbconv.
> But now it is showing as cubic box when I see the result after using
> trajconv (additionally some part of the protein is out of the box).

This could only be a visualization glitch.
Try using trjconv options.


> I do not have any clue how the box type has been changed or where could I
> go wrong.
> Please comment.
> Thank you,
> Cheers,
> Sukesh
> --
> Sukesh Chandra Gain
> TCS Innovation Labs
> Tata Consultancy Services Ltd.
> 'Deccan Park', Madhapur
> Hyderabad 500081
> Phone:  +91 40 6667 3572
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091118/f1ef6690/attachment.html>

More information about the gromacs.org_gmx-users mailing list