Re: NAMD water sphere problem

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Fri Jul 31 2009 - 19:37:50 CDT

it is very simple. spherical BC is a biasing potential in the form

U(r) = k(r-r0)^x, for r>r0

where

r0= sphericalBCr1
k= sphericalBCk1
x= sphericalBCexp1

usually quadratic potential is used, therefore x=2, constant k is
chosen arbitrary (k=10), you can leave it as is, and r0 should
correspond (or be greater) to water radius.

On Fri, Jul 31, 2009 at 6:19 PM, snoze pa<snoze.pa_at_gmail.com> wrote:
> Dear NAMD Users,
>
> I am trying to minimize a protein in using water sphere. I generated a
> water sphere big enough to merge my protein. I have the
> sphericalBCcenter coordinates but I don't know how to calculate
> following parameters
>
> sphericalBCr1
> sphericalBCk1
> sphericalBCexp1
>
> From NAMD manual I got following information.
>
> "
> * sphericalBCr1: sets the distance in at which the first
> boundary potential begins to act.
> * sphericalBCk1: The first potential applied by spherical boundary
> conditions to keep the sphere together (or pull it apart) is a
> harmonic one. This command sets the value of the force constant for
> that potential. Its value is specified in kcal/mol$\cdot$$^{2}$.
> * sphericalBCexp1: sets the value of the exponent used to
> formulate the potential; must be a positive, even integer.
>
> "
>
> But how these number are calculated is not mentioned. I saw the UBQ
> tutorial and there they are using
>
> sphericalBCr1 26.0
> sphericalBCk1 10
> sphericalBCexp1 2
>
>
> Any Idea how these numbers are calculated.
>
> I will highly appreciate your help.
>
> Regards
>
> S
>
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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