From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Tue Mar 02 2010 - 08:16:20 CST
So does this mean if you have a highly charged molecule and you are expecting it to be highly electrostatcic, do you use a big or small fullElectFrequency?
--- On Mon, 3/1/10, David Tanner <guacamoleo_at_gmail.com> wrote:
From: David Tanner <guacamoleo_at_gmail.com>
Subject: Re: namd-l: electrostatic vs van der waals
To: "Mark M Huntress" <markmh_at_bgsu.edu>
Cc: "namd-l" <namd-l_at_ks.uiuc.edu>
Date: Monday, March 1, 2010, 12:49 PM
– 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.
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
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?
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