From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Sat Sep 08 2007 - 17:06:57 CDT
I have a question regarding the use of NAMD's ABF module to calculate PMFs, where the reaction coordinate is the distance between the centers of mass of two molecules solvated in water.
In a periodically replicated system, it is clear that the PMF written to the "abf outFile" is properly scaled by r^2. i.e. this quantity is -kT log g(r), where k is Boltzmann's constant and g(r) is the radial distribution function. The PMF therefore tends to a constant value for large r and this constant can then be subtracted off as is conventionally done.
But what about systems that are not spherically symmetric - e.g. with cylindrical geometry where the solute molecules are near the boundaries? Since g(r) cannot be defined, is it correct to interpret the data in the 2nd column of "abf outFile" as -kT log P(r) (_without_ the r^2 normalization), where P(r) is the probability of occurrence of r?
I looked carefully at the original reference (Henin and Chipot, J. Chem. Phys., v121, 2904-2914, 2004), but it is not clear how the Jacobian correction is calculated in the absence of spherical symmetry in the NAMD implementation.
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