[gmx-users] peptide coming out of the box

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 20 11:30:18 CET 2007

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)


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
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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

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