**From:** Roman Petrenko (*rpetrenko_at_gmail.com*)

**Date:** Fri Jul 31 2009 - 19:37:50 CDT

**Next message:**Narender Singh Maan: "The steps in protein and membrane simulation"**Previous message:**snoze pa: "NAMD water sphere problem"**In reply to:**snoze pa: "NAMD water sphere problem"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> water sphere big enough to merge my protein. I have the
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*> sphericalBCcenter coordinates but I don't know how to calculate
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*> following parameters
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*>
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*> sphericalBCr1
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*> sphericalBCk1
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*> sphericalBCexp1
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*>
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*> From NAMD manual I got following information.
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*>
*

*> "
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*> * sphericalBCr1: sets the distance in Å at which the first
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*> boundary potential begins to act.
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*> * sphericalBCk1: The first potential applied by spherical boundary
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*> conditions to keep the sphere together (or pull it apart) is a
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*> harmonic one. This command sets the value of the force constant for
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*> that potential. Its value is specified in kcal/mol$\cdot$Å$^{2}$.
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*> * sphericalBCexp1: sets the value of the exponent used to
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*> formulate the potential; must be a positive, even integer.
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*>
*

*> "
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*>
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*> But how these number are calculated is not mentioned. I saw the UBQ
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*> tutorial and there they are using
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*>
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*> sphericalBCr1 26.0
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*> sphericalBCk1 10
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*> sphericalBCexp1 2
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*>
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*>
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*> Any Idea how these numbers are calculated.
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*>
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*> I will highly appreciate your help.
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*>
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*> Regards
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*>
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*> S
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*>
*

*>
*

-- Roman Petrenko Physics Department University of Cincinnati

**Next message:**Narender Singh Maan: "The steps in protein and membrane simulation"**Previous message:**snoze pa: "NAMD water sphere problem"**In reply to:**snoze pa: "NAMD water sphere problem"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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