[gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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