Fabian Casteblanco wrote:
Hello all,
I am setting up a free energy calculation (drug from full coulomb+vdW
in solution --> drug with only vdW in solution --> dummy drug in
solution).
After reading most of the papers, I understand that you need
significant overlap from the energies for each intermediate point to
overlap so its best to have many intermediate points from Lambda=0 to
Lambda=1. The drug molecule I have is a bit complex but I wasn't sure
if using too small of an intermediate could have a bad effect on the
free_energy calculation. I know Justin Lemkul said in its tutorial
that Lambda=+0.05 should be good for most but I decided to go with
Lambda=+0.02. Could this have any negative effect other than taking a
longer time? Also, how does one come up with the best soft-core
potential parameters to use? Is it ok to use the one from the Methane
in water tutorial?
The settings from the methane tutorial should basically be defaults, which
generally work well. Unless you have specific reason to change them, they
should be fine for most purposes.
I don't know if one can have "too much" overlap, but using BAR even 0.05 is
overkill, I've found. For methods like TI you would likely need 0.05, or even
less in some cases, but BAR converges better.
-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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