[gmx-users] Questions about g_sham options

Suman Chakrabarty suman at sscu.iisc.ernet.in
Wed Sep 2 21:57:28 CEST 2009

On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel <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.

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