trouble in dynamics

From: Sweta Ramachandran (
Date: Wed Feb 17 2010 - 23:18:48 CST

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?

II M.Sc. Genomics
C/o Dr.P.Gunasekharan,
Centre for Excellence in Genomic Sciences,
School of Biological Sciences,
Madurai Kamaraj University,
Tamil Nadu

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