Switching function while using AMBER force field

From: Sneha Menon (sneha.menon15_at_gmail.com)
Date: Wed Jan 09 2013 - 04:03:09 CST

Dear all,

I am running a NAMD simulaton using AMBER force field. I have a query
regarding the 'switching function' parameter in the NAMD configuration
file. In the NAMD User Guide, it is mentioned that 'NAMD applies switching
functions to the non-bond interactions within the cut- off distance, which
helps to improve energy conservation, while AMBER does not use switching
functions so it simply truncates the interactions at cutoff. However, if
“authentic” AMBER cutoff simulations are desired, the switching functions
could be turned off by specifying “switching off” in NAMD configuration
I would like to know what are the implications of running the simulation
with the the switching function 'on' and the same as 'off'; as far as
running NAMD simulation using the AMBER force field is concerned?

Thank you.

Sneha Menon

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:50 CST