Re: [AMBER] re-image

From: Pablo I. D. Dans Puiggr˛s <pdans.mmb.pcb.ub.es>
Date: Thu, 09 Jun 2011 15:34:54 +0200

Hi Bruno,
Try this in the same ptraj run. First center the first strand, then both:

center :1-10 mass origin
image origin center
center :1-20 mass origin
image origin center familiar

Good luck,
P.

El 09/06/2011 15:28, Bruno Rodrigues escribiˇ:
> Dear all,
>
> I'm running a normal MD simulation of a 10 base pairs DNA in a water box
> with 8A from the last atom to the border in Amber 11.
>
> However, under the course of the simulation, part of the DNA escaped from
> the box and sometimes the double strand splits and one of the parts goes to
> the next periodic cell. It is making the RMSD to jump at ery high values.
>
> I've tried all the re-imaging commands on ptraj, like *image familiar*. I
> put below some of the commands I tried in *ptraj*:
>
> *1 -
> *
> center :1-20 mass origin
> image familiar
> *
> 2 - this is the command I'm using for running the rmsd of the backbone
> *
> trajin 1D20_wat_salt10prod.binpos
> image familiar
> rms first mass out 1D20_wat_salt10prod2.rms .P,O3',O5',C3',C4',C5' time 0.2
>
> thank you in advance
> *
> *--

Pablo D. Dans Puiggr˛s, PhD
Molecular Modelling& Bioinformatics Group
Institute for Research in Biomedicine
Barcelona Science Park - Spain
pdans.mmb.pcb.ub.es
pablo.dans.irbbarcelona.org
&
Biomolecular Simulations Group
Institute Pasteur of Montevideo - Uruguay
pdans.pasteur.edu.uy



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Received on Thu Jun 09 2011 - 07:00:02 PDT
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