Re: Least squares fitting of frames of trajectory

From: Nicholas Musolino (
Date: Thu Oct 28 2010 - 08:14:39 CDT

Have you looked at VMD, the MD analysis and visualization program?

You would need to go through a tutorial or two to get started, but you can do this with an appropriate loop, and using VMD's measure RMSD fit command.

I bet there are even sample VMD scripts out there: for example,

Hope this helps.

Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT | 617-253-6675 | Room E19-528

On Oct 28, 2010, at 12:01 AM, divya nayar wrote:

> Hi,
> I am doing an MD simulation of a protein solvated with water. I want to do least-squares fitting of the frames of my trajectory against a reference structure. How can I do it in NAMD?
> Thanks in advance,
> Divya

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