From: Yaxin An (yxan2016_at_gmail.com)
Date: Thu Dec 07 2017 - 17:22:31 CST
I am running ABF simulations for the free energy of hydration of alkanes.
But I got different values for the free energies every time when I repeat
the simulations, like 1.5 and 3.0 Kcal/mol.
In the simulation, there was one water box (40 Angstrom by40 by 40). The
reaction coordinate is the Z distance between COM of the water box and the
one alkane molecule. The reaction coordinate spans from 0 to 45.
I split the reaction coordinate into 9 windows: 0-5, 5-10, ....,40-45. And
I ran the simulation in each window for 50 ns. Each time the free energy
converged. But when I repeated it, the free energy converged to a different
Hope someone can give me some suggestion.
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