[gmx-users] Re:Ka/Kd

lloyd riggs lloyd.riggs at gmx.ch
Sun Nov 11 13:47:13 CET 2012

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.


Stephan Watkins

-------- Original-Nachricht --------
> Datum: Fri, 09 Nov 2012 14:44:31 -0500
> Von: Justin Lemkul <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at 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
> ========================================
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