[gmx-users] Regarding free energy calculation

[bipin singh]

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:
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


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Regards,
Bipin Singh