[gmx-users] Questions about free energy calculation tutorial
jalemkul at vt.edu
Sun Nov 6 17:30:29 CET 2016
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
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
More information about the gromacs.org_gmx-users