Re: trouble in dynamics

From: Mert Gür (gurmert_at_gmail.com)
Date: Thu Feb 18 2010 - 04:32:18 CST

Dear Sweta,
You indicated that you used of water box with an 12 angstrom buffer. That
means that initially the protein is 24 angstroms away from its mirror image.

Imagine there is no deformation in the structure of the protein. Even if the
protein is protruding out of the water box it would be still 24 angstroms
away from its mirror image (because the mirror image makes the same move).
However if the deformation in the structre is so high that the 24 angstrom
gap is getting smaller (I don' know what your protein is) they may interact.
Can you send me a screenshot where the protein in the simulation box and the
mirror image have come close to each other .
Best,
Mert

On Thu, Feb 18, 2010 at 7:18 AM, Sweta Ramachandran <swetatty_at_gmail.com>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
> INDIA
>

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