[gmx-users] Questions about g_sham options

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 2 22:05:04 CEST 2009

Suman Chakrabarty wrote:
> On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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