# NAMD water sphere problem

From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Jul 31 2009 - 17:19:12 CDT

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 Å 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$\cdot$Å$^{2}$.
* 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

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