TMD RMSD problem

From: Elif Ozkirimli (
Date: Wed Apr 08 2009 - 15:21:16 CDT

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.


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