[gmx-users] Regarding free energy calculation

[bipin singh]

Thanks a lot for your suggestions.

On Mon, Dec 19, 2011 at 21:00, David Mobley <dmobley at gmail.com> wrote:

> 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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-- 
-----------------------
*Regards,*
Bipin Singh
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