I presume you are referring to Essential Dynamics Sampling, described in section 3.14 of the manual (v4.5.4). There is also a great tool that finds the few PCs that are maximally correlated to a functional quantity (e.g. the volume of the active site). The technique is coined Functional Mode Analysis (FMA) and you can find more information at:
http://xray.bmc.uu.se/~jochen/fma.html I have used FMA and worked pretty well in my case. I am wondering if anyone thought of using that technique to find the PCs that are maximally correlated to a functional quantity and then perform Essential Dynamics sampling on these PCs to explore the conformational space that affects the most that functional quantity. I.e. I am studying a kinase in the wt and mutant form. Although the mutation is not near the active site there is a lot of discussion in the literature about the effect of the mutation on the opening of the catalytic cleft. Some people claim that one possible explanation of the over-activity of the mutant is the greater opening of the active site, which facilitates substrate binding and thus leads to enhanced reaction turn-over. In order to test this hypothesis with unbiased MD one would need tremendous computer resources and a lot of time (the kinase is gigantic). On the other hand one could run short simulations of the wt and mutant, do FMA to find the 10-20 PCs that are maximally correlated to the volume of the active site, and then perform Essential Dynamics Sampling on these PCs to explore the conformational space that is highly correlated to the volume of the active site. After that, one could safely claim that the Hypothesis was true or false. I would be interested to read your comments on this. Thomas On 23 September 2012 11:19, James Starlight <jmsstarli...@gmail.com> wrote: > Dear Gromacs Users! > > > There are many publications about implementation of the pca-based MD > simulations for the investigation of the functional-relevant motions. > In that cases the eigenvectors are extracted from the relatively short > MD simulation of the investigated protein and than the biassed MD > simulation is started along chosen principal component which used as > the reaction coordinate. > > I'd like to know more about implementation of that technique in > Gromacs. E.g if I've performed some PCA and extracted eigenvectors how > I can run further simulation along one of the chosen PC ? > > Thanks for help > James > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists