[gmx-users] peptide coming out of the box

[Tsjerk Wassenaar]

Oh no.., not again!

Read the manual, browse the archives and try to understand periodic
boundary conditions!
(and use trjconv -fit translate or trjconv -center on your trajectory)

Tsjerk

On 3/20/07, priya priya <priyaanand_27 at yahoo.co.in> wrote:
> Dear all
>
>  I started with 6 residue peptide simulation in water for 1ns. initially i
> placed the peptide in the center using the command editconf -c flag, but
> after MD peptide is coming out of the water box. I want to calculate the
> water molecules around it and peptide interactions with water.
>
>  Is there an error running simulation.
>  Regards
>  Priya
>
>
>  ________________________________
>  Here's a new way to find what you're looking for - Yahoo! Answers
>
>
> _______________________________________________
> 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.
> 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