[gmx-users] RIMSP calculation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 28 16:56:14 CEST 2012

Hi Vijayan,

There must be a script somewhere in the archives
(http://www.mail-archive.com/gmx-users@gromacs.org/msg02871.html) that
calculates the RMSIP from the XPM file of eigenvector inner products.

> I have come across many papers where they employ RMSIP to quantify the
> similarity between PC1 and PC2 derived by essential dynamics and in
> turn use the values to prove the convergence of conformational
> sampling. Is this a well settled proposition  to drive home the point
> that the simulation has converged or should i compute the cosine
> content to prove the same. Which of this is a superior metric ?

The RMSIP only  indicates whether the subspaces sampled are similar,
nothing about the extent of sampling, and nothing about the
convergence. The "essential subspace" (ugh, ugh, cough!, pardon me)
usually converges much faster than the sampling. And the cosine
content... Well, it will show you whether the simulation did not yet
converge. Check some recent replies I gave on the list about that.



> Thanking in advance
> Regards
> Vijayan.R
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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