Re: TMD RMSD problem

From: Joshua Adelman (
Date: Wed Apr 08 2009 - 15:35:12 CDT

Are you aligning all of the frames in your trajectory before you
calculate the RMSD? If not the results will surely be different since
namd performs the alignment when it calculates the tmd force and
outputs the rmsd


On Apr 8, 2009, at 1:21 PM, Elif Ozkirimli wrote:

> Dear all,
> I am trying to use TMD to move a protein from one conformation to
> the other. I read the initial coordinates and then the target
> coordinates are read within the TMD section with the correct
> occupancy values. RMSD values are reported in the NAMD output file.
> I then try to calculate RMSD vs time for the same coordinate set
> using VMD. However, the RMSD values in the NAMD output file and
> those I calculate from VMD are different. Does anybody else have
> the same problem?
> I had poster earlier about this problem. I was hoping 2.7 would fix
> this but alas it does not.
> Any help or suggestions would be greatly appreciated.
> Elif.

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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