[gmx-users] RIMSP calculation
biovijayan at gmail.com
Thu Jun 28 17:55:01 CEST 2012
Many thanks for your kind response. Got the script, will try to run
it. Also thanks for clarifying RMSIP vs Cosine content values.
On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Vijayan,
> There must be a script somewhere in the archives
> (http://email@example.com/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
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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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