[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thanks a lot Justin,
Everything is more clear right now.
Bests

> On 06 Nov 2016, at 17:30, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 11/6/16 10:44 AM, gozde ergin wrote:
>> 
>>> This may be unstable, and is generally not done.  Turn off charges
>>> linearly, then turn off LJ with a soft-core potential (or vice versa).  The
>>> point is you should never have charges on atoms with no (or drastically
>>> reduced) LJ terms. This can be easily specified in an appropriate series of
>>> lambda states in the .mdp file.
>> 
>> So basically atomic partial charges should be reduced to zero by
>> thermodynamic integration (TI) ,than van der Waals interactions should be
>> removed from the now chargeless module in a TI calculation using a soft-core
>> LJ potential (as in you tutorial). On the other hand I do not need to use
>> soft-core in on the fist coulombic interaction calculation, right?
>> 
> 
> TI (like BAR, FEP, WHAM, etc) is a method of analysis for evaluating free energy differences.  There is no TI during the calculation.  It's a lambda-dependent scaling of the interactions, but otherwise this is correct.  One can choose to use a soft-core potential for the electrostatics, but I've never found a need for it.
> 
> -Justin
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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