Re: Re: namd trouble

From: snoze pa (
Date: Thu Feb 18 2010 - 14:08:42 CST

If protein is moving out from the box then try to move the center of
protein to origin(0,0,0).
You can use any molecular viewer like vmd/chimera/pymol/molmol to do
that. Translate protein to origin and then save it. Create new psf and
PDB files and run the simulation again.

Regarding the rotation about protein:

Use following step..

Try to minimize f
Use restrained MD to equilibrate the system for enough time.
Then run full MD.
Make sure, you are calculating correct box dimension in your
configuration file. But i guess most of the problem will be fixed if
you move your system to origin.
Good luck

On Thu, Feb 18, 2010 at 7:08 AM, Joshua Adelman <> wrote:
> 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.
> Josh
> 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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