Equilibration "substraction" from obtained PMF from MD

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Tue Jul 28 2009 - 16:32:00 CDT

Hallo to all,

I performed MD simulation of the set of small molecules in explicit
solvent and calculated PMF by ABF of 2.7b1. Molecules are prepared by
minimization of whole system(s) (molecule+solvent cluster), heating and
MD. ABF are calculated only during MD, but the equilibration period is
included in MD. Please let me know is there any way to "subtract"
equilibration period from obtained PMF. For initial definition of ABF
colvar- distances are used, as distance between two groups of atoms at
molecule(s) "ends". Molecules are flexible.

Any advice is highly appreciated.



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