Suman Chakrabarty wrote:
On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel
<[email protected] <mailto:[email protected]>> wrote:
Suman Chakrabarty wrote:
Hi, I have been trying to use the g_sham tool to generate a
histogram/free energy profile. Unfortunately a few of the output
options are not explained in the manual or "g_sham -h". These
are -dist, -histo, -bin, -map, -ls3, -mdata. Is there any way to
know further about them?
Have you looked at the output files? And the default names?
edist -> energy distribution
bindex -> bin index (I guess this meas which structure goes in which
bin)
-ls3 -> energy landscape in 3D
Just try it!
If I need to specify the number of grids in two dimensions (for
a free energy surface F(X, Y)), may I use, say, -ngrid 100 200?
It did not seem the -bw (binwidth) option can be changed along
different axes, am I right?
I tried to generate the free energy as a function of
intramolecular non-bonded interaction energy gathered in the
energy.xvg file (two column: time and energy). The energy values
range from -300 to 0 KJ/mol. But when I try the following
command: g_sham -f energy.xvg -ls gibbs.xpm, 3 files are
generated: bindex.ndx, ener.xvg and shamlog.log. I am confused
with the file ener.xvg since the X-axis ranges from 0 to 30!
What is contained in this file?
Good question, but you probably need to supply a bit more info to
get something interesting...
My energy.xvg file contains the output from g_energy where first column
is time and second column is LJ short range interaction energy
(LJ-SR:Protein Protein). The values of energy are distributed between
-300 to 0 KJ/mol. So I expect a histogram or free energy as a function
of this energy, where X-axis values would range from -300 to 0 KJ/mol.
But when I try the above command, or simply "g_sham -f energy.xvg" the
screen output says:
Read 1 sets of 3584 points, dt = 1
There are 32 bins in the 1-dimensional histogram. Beta-Emin = 0
Ptot = 3584
The output file ener.xvg looks like a free energy surface (1D), but the
X-axis values range from 0 to 30, instead of -300 to 0.
I am not sure whether ener.xvg is supposed to contain the free energy or
not. But even if I try with "-ls gibbs.xpm" option, no gibbs.xpm file
comes as output. Probably that is only relevant for 2D free enegry surfaces?
Any suggestion? Thanks.
OK, I think I understand. Since the free energy is based on simple
counting, the minimum is by definition zero, and the max level is
determined by the amount of points (-kB T ln (1/Pmax)) where Pmax is the
number of points in the largest bin.
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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