Re: namd trouble

From: Joshua Adelman (
Date: Thu Feb 18 2010 - 07:08:46 CST

Hi Sweta,

Please don't email people off-list. If some is still active in the community then they'll get the email when you send it to the list.

As Mert similarly pointed out, unless your protein is unfolding or undergoing a large conformational change, given that you padded the protein with 12 A of water, then they shouldn't be interacting. You could also run into a problem if you have an oblong protein in a rectangular box with dramatically unequal lengths, and then the protein rotates. But all of these things seem unlikely for a stable protein in only 0.25 ns of simulation time. It's hard to say though without knowing anything about your particular system.


On Feb 18, 2010, at 3:36 AM, Sweta Ramachandran wrote:

> Dear sir,
> I found your mail id in one of those threads at ks. 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 imaged 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?
> Thank you for your time. Waiting for your reply
> Regards
> Sweta
> --
> 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

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