[gmx-users] Re: Free energy calculation question

[Fabian Casteblanco]

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
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.

Thanks for your help.
-Fabian

On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
<fabian.casteblanco at 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.casteblanco at gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com