FEP with flattened free energy surface?

From: Ivan Vyalov (VyalovIvan_at_yandex.ru)
Date: Wed Apr 06 2011 - 04:49:50 CDT

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Hi all,

I wonder, is it possible to perform FEP calculations with solute molecule with flattened free energy surface along several reaction coordinates?

For instance, if I take dipeptide with conformational degrees of freedom ( dihedrals \phi & \psi ) and two minima defined by them, I should take into account this minima and do something similiar to what is described in JPhysChem 97, 3409.

>From the other hand I could run ABF, apply forces and perform FEP with flat free energy surface along these coordinates, is it possible in NAMD? Or I should do such task in a different way?

-- 
with best regards,
Ivan

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