[gmx-users] Re: problem in binding free energy calculation and setting Lambda

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 27 19:38:54 CEST 2011

meisam valizadeh kiamahalleh wrote:
>     Dear Marcelo 
> Thank you very much for you kind reply.
> Actually, I am following Justin Lemuk's tutorial. He used pear script to 
> do all simulations in one setting. Unlike him, I want to do each one 
> separately and unfortunately, I couldn't get any info for my second 
> question which is about setting initial and final Lambda for my energy 
> stuff in each simulation. Could you please help me which parameters I 
> need to change for each step?

The Perl scripts write the files you need to complete the tutorial.  You can 
then run as many of the resulting Bash scripts to execute the simulation(s) for 
individual lambda values.  The theoretical background is all explained in the 
tutorial.  You need to do a transformation between lambda = 0 and lambda = 1, 
with sufficient intermediate values to get good overlap of the free energy 
histograms (also explained in the tutorial).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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