TMD SIMULATION - RMSD DOUBT

From: Semorale (semorale_at_gmail.com)
Date: Tue Jul 08 2008 - 20:05:37 CDT

Hi all!!

I realize a targeted MD simulation . On having analyzed the results, I find
with some "surprises" that I would like to help me to resolve:
1.-On having initiated the simulation, NAMD indicates that the RMSD of TMD
simulation is 14, and diminishing (as it must be in TMD). But when I
graphical the RMSD of the trayectory in VMD (RMSD trayectory tool), the
RMSD:
a) It goes in increase
b) it never reaches 14, only reaches 4

Why the RMSD so different?... At best cases, the graph in VMD should begin
in 4 and to reaches to 0, but it is on the contrary.

2.-NAMD indicates that on having finished the simulation (3ns), the RMSD is
virtually 0 (0.000103125), which means that it reach the final structure.
Nevertheless, on having observed the path, it does not appreciate that the
final structure is reached. Why is this? ? Is it a convergence problem of
TMD in NAMD? Is simulation very short time?

Any suggestion to me is useful.
Thanks in advance

SAMUEL

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