Thanks for the clarification!
Yes, periodic boundary conditions were applied. Is the nmode module in NAB the same as the standalone nmode? Can it handle the PBC in the 2nd derivative calculation?
Best
JT
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: John Travers <jtravers70.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, August 10, 2013 9:30 AM
Subject: Re: [AMBER] output nuclear force and hessian
On Fri, Aug 09, 2013, John Travers wrote:
>
> 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!
You don't give many details about what you did, but here is a guess: If the
"molecule in a solvent" calculation used periodic boundary conditions, then
what you see is to be expected: nmode has no capability to handle periodicity,
and will give incorrect results if the simulation was run with PBC turned on.
...dac
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Received on Sat Aug 10 2013 - 15:30:02 PDT
