[gmx-users] peptide coming out of the box

Berk Hess gmx3 at hotmail.com
Tue Mar 20 12:00:25 CET 2007


Maybe we should let people do a test before they can become member
of the mailing list. We already have two questions:
Can you search the list archive?
It is a problem when a peptide comes out of the box?

Berk.

>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] peptide coming out of the box
>Date: Tue, 20 Mar 2007 11:30:18 +0100
>
>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
>>
>>
>>  ________________________________
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>>
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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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