Seeking suggestions to decide on realistic configuration values

From: S.K. Ghosh (
Date: Thu Jun 12 2008 - 14:40:27 CDT

Hi NAMD users,

I am trying to build up a close to realistic simulation of
biotin-streptavidin in water. The charge on the molecule is -4 (-1 for each
segment of streptavidin). Is this so large that ions need to be placed in
water to make the system neutral and stable?

Is timestep 1.0 realistically good? Or should I go for timestep 0.5?

Also could you please comment whether the following values (as in the
tutorial)good for realistic cases.

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switchdist 10.
pairlistdist 13.5
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
langevinDamping 1
langevinHydrogen off
sphericalBCr1 26.0
sphericalBCk1 10

Your suggestions would be extremely helpful and much appreciated.


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