Re: trouble in dynamics

From: Andreas Förster (
Date: Thu Feb 18 2010 - 04:54:31 CST

Dear Sweta,

first off, I hope you don't really have a mirror image of your protein
in your simulation. You shouldn't mix L- and D-amino acids.

Since your water box is infinitely repeated for the purpose of the
simulation, it probably doesn't matter that your proteins sticks out.
It reenters the box on the other side, and all is good. If you see
interactions between the master copy of your model and models in
equivalent positions in adjacent cells, your water box might be too
small. Start with something bigger.


On 18/02/2010 5:18, Sweta Ramachandran wrote:
> Dear all,
> I was wondering if you could help me with a problem that I am facing
> while running productive dynamics for my protein.
> I solvated my protein in a water box with a thickness of 12 angstrom.
> after it finished running for 0.25ns, a small part of the protein is now
> protruding out of the water box. when i tried running the trajectory
> file, I can see that the protein in the simulation box and the mirror
> image have come close to each other in all the three axes- X,Y and Z and
> the proteins are interacting with each other.
> Can you please suggest what I should do further as protein interacting
> with protein is not desirable?
> --
> Regards,
> Sweta.R
> II M.Sc. Genomics
> C/o Dr.P.Gunasekharan,
> Centre for Excellence in Genomic Sciences,
> School of Biological Sciences,
> Madurai Kamaraj University,
> Madurai-625021
> Tamil Nadu

         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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