Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials

From: David A Case <>
Date: Tue, 17 Sep 2013 16:05:52 -0400

On Tue, Sep 17, 2013, Ryan Muraglia wrote:
> One of my sanity checks was to run the TI scheme "backwards," meaning that
> in the groupfile, I flipped the order of the sander calls.

Are you sure that everything (initial coordinates, initial velocities, etc.)
is the same in the two runs? The usual debugging rules apply here: run
a short (say 20-step) MD run, with ntpr=1 and lambda=0.5. Do you see the
mirror-image behavior? Are the potential and kinetic energies the same
at the first step? At later steps? Does anything change if you set ntt=0?

Lots of things can cause two trajectories to get out of sync, but you can
probably track it down with a number of very short runs. TI in sander *is*
just a matter of running on a mixed potential surface and collecting
statistics, so things should match up.

...good luck...dac

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Received on Tue Sep 17 2013 - 13:30:02 PDT
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