[gmx-users] trjconv -pbc?

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 21 20:02:09 CEST 2007

Hi Belquis,

You have to give trjconv a reference structure in which the parts are
together and which is close to the starting configuration. This has
been mentioned on the list before. For more information, search the
archives on trjconv and/or periodic boundary conditions (and possibly
my name).



On 6/21/07, bmmothan at ucalgary.ca <bmmothan at ucalgary.ca> wrote:
> Hello all,
> I have tried using trjconv -pbc(all options) to get a continuous
> trjactoary visulations on VMD.  I am modeling an 11 residue receptor
> antiparellel to itself and one of the receptor strand jumps outside the
> box sometimes.
> I have used search to solve the problem but everthing i tried didnt work
> and the -pbc just makes it worse.
> I tried using the -pbc nojump alone and this made my two receptor strands
> away from each other all the way (one inside and one outside the box).
> However i want them to be close together since they are hydrogen bonded.
> I have also tried: nojump then whole; whole then nojump and they make the
> receptor just fly around or pieces of it stretch.
> anyhelp is appreciated.
> Belquis
> _______________________________________________
> 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

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list