Fabian Casteblanco wrote:
Hello Justin,
I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling. So if I take the line formed by dGtotal vs Lambda from
g_bar output and take the derivative excluding the beginning and end
parts (lambda approaches 0 and 1) then it does seem to take more of a
somewhat linear shape. If you can see attached, I think perhaps thats
You haven't attached anything.
how I was misreading it? I hope that can be the reason, since I've
done it with 4 different cases (2 different amount of solvent
molecules and using MD and SD integrator) and they all seem to be
giving similar results.
That could be it. The BAR output and the plots from TI are different. Also be
sure that you're not using soft-core for the Coulombic (de)coupling, as was
suggested previously.
-Justin
Thanks for your help.
-Fabian
On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
<fabian.castebla...@gmail.com> wrote:
Hello Justin,
I'm calculating the free energy of a drug in an alcohol solvent. I
have a question referring to your free energy tutorial. You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary. Is this true for your case of methanol in water or
for all cases? When I ran my system of drug in ethanol solvent, I got
a non linear dG for both electrostatic and vdW. Also, is there no
need to find dG of cav ( the free energy required to form the solute
cavity within the solvent) ? I have attached some graphs.
Thanks for your help. Your tutorial was extremely useful.
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.castebla...@gmail.com
--
========================================
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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