AMBER Archive (2003)

Subject: Re: SANDER vs GIBBS equilibration

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Mar 27 2003 - 14:58:58 CST

I've had _extremely_ hard time equilibrating
such systems (in the past) due to the small
size and the fact that almost nothing collides
with the ring substituents to redistribute energy
while they are disappearing. in some cases the gas
phase calculation was much more than an order of
magnitude slower to converge than in solution.
try plotting the dihedral angle of the hydroxyl
rotation during the perturbation and make sure you
don't see unexpected changes in the transition rates.
you may need to modify how you are doing the
coupling to the bath.
carlos

> On Wed, Mar 26, 2003, Sophia Kondratova wrote:
>
> > I have noticed something peculiar while trying to perform an FEP
> > simulation of phenol --> benzene in gas phase using the GIBBS module
> > of AMBER7.
>