restraint potential used in the ABF calculations

From: chengh_at_ringo.chem.pitt.edu
Date: Tue Mar 23 2010 - 13:36:22 CDT

Hi all,

I am doing ABF calculation of 1D PMF for an ion f(z). I would like to use
some sort of cylindrical confine potential to restrain the ion movement on
the xy plane, but no restraint on z direction. I do the following way

constraints on
consRef restrain_ion.pdb
consKFile restrain_ion.pdb
consKCol o

selectConstraints on
selectConstrX on
selectConstrY on

This way the ion movement along the xy plane will be restrained, but not z
direction. Any potential problem with this restraint for the calculation
of f(z)? If so, any suggestions for how to use cylindrical restraint
potential for this type of the PMF calculations.

Many thanks,

Mary

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