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.
Regards
Sangeeta
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