Re: restraint potential used in the ABF calculations

From: Giacomo Fiorin (
Date: Tue Mar 23 2010 - 17:41:11 CDT

Hi Mary, the setup you're using will work, but ideally, you may prefer
to not apply any constraint force along x and y up to a certain
distance from the channel axis.

if you use the new ABF implementation inside the collective variables
module (NAMD 2.7b1 and following), you can define one "distanceZ"
variable like the one you were using, with boundary potentials above
and below the channel. And add to it another one, this time of
"distanceXY" type, with a boundary potential above a few . This way
the ion would be confined inside a cylinder. Then in the ABF
configuration, you just specify to use the first variable for a 1-d
PMF, unless you want to try a 2-D PMF (which is also now supported).


---- ----
 Giacomo Fiorin
   ICMS - Institute for Computational Molecular Science
     Temple University
     1900 N 12 th Street, Philadelphia, PA 19122
 work phone: (+1)-215-204-4216
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On Tue, Mar 23, 2010 at 2:36 PM, <> wrote:
> 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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