[gmx-users] Questions about free energy calculation tutorial

gozde ergin gozdeeergin at gmail.com
Sun Nov 6 16:44:11 CET 2016

> 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?

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