[gmx-users] A matter on outputting trajectory of gromacs 4.0

[Justin A. Lemkul]

G.H. Zuo wrote:
> Dear Gromacs Users
> 
> I download the new gromacs 4.0 and do some tests on protein folding.
> It seem that there is a matter on outputting trajectory in this version.
> When the protein is at the boundary of the box, the mdrun will output the
> protein in some segments.  This matter had never found in the preview
> versions.  And It seem that the program trjconv can't correct this matter.
> Is there someone having ideas about this?

I reported this as well, and it has to do with the new domain decomposition 
scheme (thanks, Tsjerk).

http://www.gromacs.org/pipermail/gmx-users/2008-October/036920.html

And yes, trjconv *does* fix the broken molecules; use trjconv -pbc whole with 
your .tpr file.

-Justin

> 
> thanks
> 
> Guanghong
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================