question about nonnbonded parameters

From: Leonardo Sepulveda Durán (
Date: Tue May 31 2005 - 11:04:23 CDT

Hello, I would like to ask some questions about nonbonded parameters I
havent grasp completely yet. As I undestood:

1) stepspercycle is the number of timesteps beetween atom
reasignments, then is the number of timesteps beetween the pairlists
are regenerated.
2) pairlistpercycle is the number of times pairlists are regenerated
in a cycle. So if I have
stepspercycle = 20
pairlistpercycle = 2

is the same using

stepspercycle = 10
pairlistpercycle = 1

3) outputPairlists say to redefine pairlists for an atom if some of
their list partners move further than (pairlistdist -cutoff)/2,
similar to heuristic option in CHARMM nonbond parameters. So using
outputPairlists=1000 will enable heuristic atom reasignment and will
print warnings every 1000 timesteps. Nevertheless in the manual, says
heuristic criteria is (pairlistdist -cutoff)/2 only at the begining,
but is reasigned with other criteria later. So I am not sure if
heuristic method is default and "outputPairlists" only prints the
warnings, or if it actually defines the use of an heuristic update
intead of constant-timestep updating.



This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:48 CST