From: Nicholas Musolino (musolino_at_mit.edu)
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,
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node185.html
Hope this helps.
Nicholas
---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:41 CST