AMBER Archive (2002)

Subject: Re: Strange MD simulation results with GB solvation at high temp.

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Wed Sep 11 2002 - 21:04:44 CDT

As a side note, we've been looking atthe effect of using a cutoff
(in proteins, AMBER7 with GB solvation). We find essentially no
correlation between relative energies of a set of structures without
cutoff and with cutoffs ranging anywhere from 8A to 20A
(using the same set of structures in each case). We are working on a
fix for this but the strongly suggest not using a cutoff with GB.

Carlos

From: "David A. Case" <case_at_scripps.edu>
> I don't know if this is related to your problem, but using the default
cutoff
> (8 Ang.) is only recommended for PME calculations. Certainly a longer
cutoff
> would be needed for good simulations with gb.