Hi,
I had another strange observation for the forces computed by nmode and sander. For a molecule in solvent, I performed a microcanonical dynamics. I found the the forces on the solute molecule obtained from these two code agree reasonably well, the difference < 10%. However, the forces on solvent molecules show large disparity, often > 50%. Are these difference still resulted from the different implementation and different algorithms? Thanks!
Best�
JT
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: John Travers <jtravers70.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, August 7, 2013 2:41 PM
Subject: Re: [AMBER] output nuclear force and hessian
On Wed, Aug 7, 2013 at 12:49 PM, John Travers <jtravers70.yahoo.com> wrote:
> Thanks!� I made the modifications to output nuclear cartesian forces in
> runmd.F90 and nmode.F90. For the force, the outputs from these two
> subroutines are slightly different. For example, I made an test on an
> isolated benzene molecule, the forces (for the 1st C) from runmd and nmode
> are " -0.1505921505018395E+01 -0.2234835466490895E+01
>� 0.4347184130879028E+00" and " -0.1505920513395167E+01
> -0.2234834582828459E+01� 0.4347184163951585E+00".
>
> Does anyone know the reason for this?
>
Computers ;).� The force field is implemented differently for nmode and
sander, meaning that the order of operations will be different and errors
will accumulate -- especially in quantities like the forces where you're
adding contributions from a bunch of different force field terms.
Also, nmode and sander compute torsion terms fundamentally differently.
While both approaches are mathematically equivalent, the finite numerical
precision consequences are more ambiguous.� These numbers appear to agree
quite well.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 09 2013 - 20:30:02 PDT