Re: SWM4-NDP Simulation

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Aug 24 2011 - 18:49:22 CDT

Dear Dave,

I'll see if I can answer:

1) drudeBondConst should be used with drudeBondLen - these put an additional quartic restraining force on the Drude oscillator using constant drudeBondConst if the bond length is greater than drudeBondLen. Note that drudeBondConst is not the Drude spring constant, which should already be defined in the force field parameters file.

2) For a Drude simulation, the NAMD TEMP value will be lower than the target temperature because it tries to average both the cold and warm degrees of freedom. With Drude turned on, you will also see DRUDECOM (center-of-mass temperature) which should gradually approach 300K from below and the DRUDEBOND (oscillator temperature) which should even more gradually approach 1K from above (although it might never get any lower than 5K).

Hope this helps.

-Dave

On Aug 24, 2011, at 2:49 PM, David Huggins wrote:

> I am simulating water with the SWM4-NDP model. I have two questions.
>
> 1) What should the drudeBondConst value be set to? 1000?
> 2) I am trying to use temperature and pressure controls to keep the simulation at 300K and 1 bar, but the temperature fluctuates around 200K. Is this an error in the temperature reporting due to the drude particle being at 1K or a problem with the simulation?
>
> Thanks,
>
> Dave
>
>
>
>

--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/

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