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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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