On 11/11/12 7:47 AM, lloyd riggs wrote:
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.
Framework for parallelizing analysis tools is in the works, with a target of
version 5.0 for implementation, since the code is undergoing a major overhaul
for that release, anyway. It will be a long time before that release, though,
but it's in the works.
-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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