[gmx-users] query about free energy landscape

sangeeta kundu sangeeta0983 at yahoo.co.in
Fri Feb 26 06:59:06 CET 2010

Dear Sir, 
            I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape. The free energy = -KBTln(probability of conformational distribution). But I can not understand how to find the conformational distribution, is it already embedded in the algorithm of g_sham? 
I followed the following procedure mentioned below. 
First I prepared an xvg file with 3 columns; the first is the time frame, 2nd and 3rd parameters are the parameters I want to calculate, for eg the projections along 1st and 2nd Principal Components.  
Then I used the command  
g_sham –f  *.xvg  -ls 
Then I converted gibbs.xpm into an eps file using xpm2ps –rainbow. The file that I obtained is not showing free energy landscape, rather an eps file is generated which contains some scattered square like conformations. Please suggest If I am doing anything wrong. Should I follow the same procedure while generating the FEL using other variables like potential energy, Rg or RMSD? 
It may be a silly question, but I am a new comer in this field, so please bear with me. Your urgent help in this matter is highly appreciated. 

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