[gmx-users] Re: gmx-users Digest, Vol 71, Issue 37 (Calculating Binding Affinity between Protein and Ligand using FEP)

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 10 13:07:57 CET 2010

sunita gupta wrote:
> Thanks Justin
> After going through the discussion on mailing list I got to know that 
> "coulombic and LJ interections has to be decoupled separately and for 
> better scaling Lambda should have closer values. But my query is that 
> for what value of lambda LJ has to be decoupled and for values of lambda 
> coulombic interactions has to be decoupled.
> Like if I am having 11 lambda values ranging from 0 to 1...with 
> successive increase of 0.1, what range of of lambda should have
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw
> (...to decouple only Coulombic interactions)
> and what lambda values should have
> couple-lambda0 = vdw
> couple-lambda1 = none
> (...to decouple van der Waals)
> And what should be the value of couple-intramol:
> Thanks in Advance

There are numerous papers that describe procedures suitable procedures for 
calculating ligand binding energy with free energy calculations.  I suggest you 
start there.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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