Dear Justin, Thanks, Just a normal delta G then. I wondered if it also was doing a matrices from 2 columns if you supply something like just the 2d output from covar/anaeig (PCA). I did find a simple python 6 liner for just doing PCA with the first (or any 2) derivatives just using numpy, and some module written by tsjerk Wassenaar posted a few years ago (a Gromacs plugin called g_entropy) which all together seem to meet my needs. Also (the above person) has a number of small python scripts for Gromacs for matirces, PCA, and just turning .xpm data from g_sham into a number matrices to put into a plotting tool (such as Scidavis or something). There on a web page, and a few dozen just scattered in older gromacs postings.
If I had a request for Gromacs dev though it would be to multithread the vector portions of the analytical tools. A single Intel i7 or AMD only uses one of the 8 cores, so it takes several hours, for each component times each of however trajectories are looked at. Most everything else is a minute or two only using a single core. Sincerely, Stephan Watkins -------- Original-Nachricht -------- > Datum: Fri, 09 Nov 2012 14:44:31 -0500 > Von: Justin Lemkul <jalem...@vt.edu> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Re:Ka/Kd > > > On 11/9/12 1:02 PM, lloyd riggs wrote: > > Dear All, > > > > Reguarding a question I asked below. Does anyone know what the > formulei, etc...are for g_sham taking in 2 columns (or 3 with time) and > turning it > into a density matrix. Is it just a count, summation on x-y or other? > > > > Values are divided into histograms and calculated by dG = -RT ln (P - P0), > where > P0 is the histogram bin with the largest probability such that the value > of dG > is set to zero here and all other values are relative to it. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- 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
