Dear Thomas Steinbrecher
I apologize for my many questions.
In Results section of tutorial you said: The free energy change associated
with each of the steps can be calculated by numerically integrating over
the &Delta (Complex-Water) curves on the right from &lambda=0-1. The
integration can e.g. be done using this
script<
http://ambermd.org/tutorials/advanced/tutorial9/calc_dvdl.pl>on
a list with &lambda, dV/d&labda and rms(dV/d&lambda) values like that
one <
http://ambermd.org/tutorials/advanced/tutorial9/result_vdw.dat>)
*0.1000 -2.9742 3.7806*
*0.2000 -1.8932 3.6766*
*0.3000 -0.1558 3.6142*
*0.4000 1.4523 3.8781*
*0.5000 2.7927 4.3757*
*0.6000 2.7280 4.8655*
*0.7000 3.5548 4.6119*
*0.8000 2.7449 4.2764*
*0.9000 6.1854 4.6211*
I want to know this data are about what step? Step 2? For reaching final
conclusion in tutorial Step Free Energy
change
Delta G (Step 1) 0.05 Delta G (Step 2)
1.72 Delta G (Step 3) 0.06 Delta G (Total)
1.83I will do following steps: 1) For each
step, I will calculate (DVDL complex - DVDL water). 2) I will obtain delta
G each step using numerical integration. But I have not DVDL relating to
lambda = 0 and 1. You mentioned “the parameter lambda was set to 0.1, 0.2,
..., 0.9”. You didn’t use lambda 0 and 1. Why? Also, you said “The
trapezoid rule (values for &lambda=0 and 1 were linearly extrapolated from
the closest two values)”. Please explain more. Best regards
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Received on Sun Dec 04 2011 - 04:30:03 PST
