AMBER: Cut off for cavities

From: Sangwai, Ashishvikas <>
Date: Mon, 2 Apr 2007 13:47:30 -0500

I have created a 'near hard sphere potential' for a cavity to be simulated in SPCE water using L-J interaction with cavity-water as epsilon = 0.001
The thermal radius of cavity-water is needed to be 9 Ang for the purpose. For which the van der waals radius of cavity (sigma) becomes = 23 Ang.
Therefore the radius amber accepts in frcmod file (sigma*) becomes 23*2^(1/6)*(1/2) = 13 Ang.
My question is what should be the cut-off radius for potential calculation. Should that be more than sigma 23 Ang. or more than sigma* 13 Ang.?
Thanks very much.
Ashish Sangwai

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Apr 04 2007 - 06:07:28 PDT
Custom Search