Re: electrostatic vs van der waals

From: David Tanner (guacamoleo_at_gmail.com)
Date: Mon Mar 01 2010 - 11:49:07 CST

– nonbondedFreq: how often to calculate the pairwise interactions;
AKA interactions within cutoff
– fullElectFrequency: how often to employ the long range PME
electrostatic calculation; AKA interactions beyond cutoff
The frequencies you refer to below (1-2-4) are reasonable.
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David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
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On Mar 1, 2010, at 9:57 AM, Mark M Huntress wrote:

I am curious, I am trying to set nonbondedFreq and fullElectFrequency.
The manual says this:

– nonbondedFreq: specifies in number of time steps how often
nonbonded interactions should be calculated. It is useful for
saving computational time.
– fullElectFrequency: specifies in number of time steps how of-
ten full electrostatic interactions should be calculated.

what exactly is the difference between these two? Are the interactions
of atomic point charges included in the nonbonded interactions?
I mean, what all is calculated in non-bonded?

If I am running MD just to get a realistic solvent configuration, with
TIP3P waters, would nonbondedfreq =2 and fullelectfreq = 4 be
appropriate or should I make the calculations more frequent?
Thanks,
Mark

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