**From:** Jason O'Young (*joyoung_at_uwo.ca*)

**Date:** Thu Sep 20 2007 - 14:41:00 CDT

**Next message:**Arun Krishnan: "Re: Temperature dependent unfolding.."**Previous message:**David Hardy: "Re: Switching Function"**In reply to:**David Hardy: "Re: Switching Function"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thanks Dave!

In that case, what are commonly used switchdist and cutoff parameters?

To my understanding, the GROMACS defaults for the analogous

parameters are 0 and 10 (I am trying to run a GROMACS simulation in

NAMD). As a result, I just chose a small value to replicate it as I

could not use 0. However I am unsure how they handle their switching

function.

Cheers,

Jason

On 20-Sep-07, at 2:39 PM, David Hardy wrote:

*> Jason,
*

*>
*

*> The switched potential has the form: U(r) s(r),
*

*>
*

*> where U(r) is your unmodified Lennard-Jones potential
*

*> and s(r) is a smooth, piecewise defined polynomial:
*

*>
*

*> s(r) = 1 for r <= switchdist
*

*> s(r) = 0 for r >= cutoff
*

*> otherwise, s(r) is a decreasing function
*

*>
*

*> So there is no danger of the function being entirely positive,
*

*> although your choice of switchdist will probably give you a much
*

*> shallower well depth than you want.
*

*>
*

*> Regards,
*

*> Dave
*

*>
*

*>
*

*> On Sep 20, 2007, at 1:00 PM, Jason O'Young wrote:
*

*>
*

*>> Hi All,
*

*>>
*

*>> I set my switchdist to 0.01 and my cutoff to 10.
*

*>>
*

*>> I am not too sure how the switching function would look like, but
*

*>> is there a danger of the function being entirely positive?
*

*>>
*

*>> For an example of what I mean, see this picture from the users guide:
*

*>> http://www.ks.uiuc.edu/Research/namd/2.6/ug/img14.png
*

*>>
*

*>> If the switching was to begin at such a low value, would the
*

*>> function just proceed from infinitely positive to 0? Or would the
*

*>> general form of the potential function be "squeezed"?
*

*>>
*

*>> Thanks in advance!
*

*>> Jason
*

*>>
*

*> ----------------------------------------------------------
*

*> David J. Hardy, PhD
*

*> Theoretical and Computational Biophysics
*

*> Beckman Institute, University of Illinois
*

*> dhardy_at_ks.uiuc.edu
*

*> http://www.ks.uiuc.edu/~dhardy/
*

*>
*

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