From: Myunggi Yi (
Date: Wed Feb 03 2010 - 09:33:08 CST

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
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:44 CST