From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Feb 03 2010 - 10:07:36 CST
With your stated configuration parameters, the bonded interactions
are evaluated using a timestep of 1.0 fs, the short-range non-bonded
interactions are evaluated using a timestep of 2*1.0 = 2.0 fs, and
the long-range electrostatics are evaluated using a timestep of 4*1.0
= 4.0 fs.
On Feb 3, 2010, at 9:33 AM, Myunggi Yi wrote:
> Dear NAMD users,
> I am so confused by the manual about the update of the pair list of
> non-bonded interactions.
> If the followings are the simulation parameters, what is the update
> frequency of the pair list of non-bonded interactions?
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5 # Description: A pair list
> is generated pairlistsPerCycle times each cycle
> timestep 1.0
> rigidBonds all
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20 # Description: Number of
> timesteps in each cycle. Each cycle represents the number of
> timesteps between atom reassignments.
> pairlistspercycle 2 # Description: Rather than
> only regenerating the pairlist at the beginning of a cycle,
> regenerate multiple times in order to better balance the costs of
> atom migration, pairlist generation, and larger pairlists.
> Thank you.
> Best wishes,
> Myunggi Yi
> 91 Chieftan Way
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
> Office: +1-850-645-1334
-- 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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