Re: TMD SIMULATION - RMSD DOUBT

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Jul 08 2008 - 22:04:51 CDT

Samuel,

Two things to consider:
1. TMD does an alignment of the current structure with the target
structure, so if in VMD you are doing RMSD without aligning each frame
to the target frame you're going to get different answers.
2. There were some problems with the MPI vs serial version of TMD in
NAMD:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5928.html
I believe the problem was corrected in the CVS version but not the
distributed executable.

Josh

On Jul 8, 2008, at 6:05 PM, Semorale wrote:

> 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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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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