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
