[AMBER] SMD average work

From: Mahmood Jasim <ddfd09.gmail.com>
Date: Tue, 3 Mar 2015 15:58:09 +0000

Hi AMBER users,

I performing a steered MD calculations with 20 simulations on 20 starting
structures of the same system. I am following the formation of a covalent
bond with QM treatment for the region involving the formation of the bond.
My reaction coordinate is an LCOD.

My questions may sound stupid so forgive me. How should I calculate the
average work across all the simualtions? Is it a simple numerical average
or should it be expontential?

Another questions; should I average the LCOD values as well? Although they
are very similar between the simulations, they are not identical. The
starting structures came from a conventional MD run in which the reaction
coordinate was constrained.

Mahmood Jasim
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Received on Tue Mar 03 2015 - 08:30:02 PST
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