Hi Gromacs users I am trying to measure the similarity of the subspace sampled by a mutant protein-Ligand complex versus a wild type complex based on the eigen vectors computed using PCA.
I was wondering, does and handy scripts does exists to compute the root mean square inner product ( RMSIP). It would be really thankful if any one could provide me a script for RMSIP calculation or kindly let me know if there exists any way to compute RMSIP directly using Gromacs. My second question is ( sorry as this is a general question) 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 ? Thanking in advance Regards Vijayan.R -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
