[gmx-users] Questions about g_sham options

Suman Chakrabarty suman at sscu.iisc.ernet.in
Wed Sep 2 17:07:54 CEST 2009

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?

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

What am I doing wrong? What would be the right way to generate the free
energy surface for both 1- and 2-dimensional cases? Thanks.

Suman Chakrabarty.
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