[gmx-users] Regarding free energy calculation

[Justin A. Lemkul]

bipin singh wrote:
> Hello,
> 
> I am willing to study the free energy of binding of a cation (Ca++) to
> the protein and I am following the free energy tutorial
> provided by Justin
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy
> ).
> Please let me know whether the settings for this type of study would
> be same as given in the tutorial for ligand-Protein
> binding free energy calculation or it need some different approach:

By decoupling a Ca2+ ion, you are removing 2 charges from the system.  I don't 
know how to properly treat such a case (perhaps someone else can comment), but 
likely you'll find such topics in the literature.  A better approach may be 
umbrella sampling, but again the literature should point you to reasonable 
methodology.  I'm sure others have dealt with such questions before.

-Justin

> The setting from the ligand-Protein binding free energy calculation
> are given as:
> 
> 
>  van der Waals coupling:
> 
>      sc-alpha          = 0.5     ; use soft-core for LJ (de)coupling
>      sc-sigma          = 0.3
>      sc-power          = 1
>      couple-moltype    = LIG
>      couple-intramol   = no
>      couple-lambda0    = none    ; non-interacting dummy in state A
>      couple-lambda1    = vdw     ; only vdW terms on in state B
> 
> Coulombic coupling:
> 
>      sc-alpha          = 0       ; soft-core during (dis)charging can
> be unstable!
>      sc-sigma          = 0
>      couple-moltype    = LIG
>      couple-intramol   = no
>      couple-lambda0    = vdw     ; only vdW terms in state A (the
> previous state B is now A)
>      couple-lambda1    = vdw-q   ; all nonbonded interactions are on in state B
> 
> 

-- 
========================================

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

========================================