[gmx-users] Regarding free energy calculation

[David Mobley]

Yes, changing the net charge of the system is something that is rather
complicated in fact (one can plunge ahead and do it while ignoring the
complications, but the results will typically be rather system-size
dependent and essentially wrong). For more details refer to the Kastenholz
and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references
therein. The good news is that for simple spherical ions K&H have worked
out the relevant corrections. The bad news is that if you move away from
simple spherical ions you've got problems.

David Mobley



On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
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-- 
David Mobley
dmobley at gmail.com
504-383-3662
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