[gmx-users] Free energy calculation question

[Justin A. Lemkul]

Fabian Casteblanco 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

I've never seen a case where (de)coupling of Coulombic interactions wasn't 
linear.  Since, for electrostatics, V is linearly dependent on lambda, I would 
expect this to generally be the case.  I don't know if nonlinearity is possible; 
maybe someone else can comment.  But generally, people use very few lambda 
values when (de)coupling charges from the system and linearity is generally 
achieved, with some minor variation towards the extreme values of lambda (close 
to 0 and 1).

> 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.
> 

There is no explicit cavity term, but that's what happens when you turn on LJ 
interactions - the solute appears gradually within the solvent.

-Justin

-- 
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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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