[gmx-users] Questions about g_sham options

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 2 17:38:37 CEST 2009

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...

> 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.
> Regards,
> Suman Chakrabarty.
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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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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