Re: [AMBER] running NAMD with AMBER inputs

From: David Case <>
Date: Sun, 1 Sep 2019 20:00:43 +0000

On Sun, Sep 01, 2019, Rui Chen wrote:
>I am running MD simulation with AMBER inputs, please find attached my
>configuration file. Since in AMBER force field, the switching function is
>turning off, the result will be less accurate. I found a template from NAMD
>user's guide and another example, both of them have a cutoff value 9.0. If
>I increase the cutoff to a large number (say, 999), will I increase the
>accuracy of the simulation?

The maximum value of the cutoff is (roughly) half the length of the
smallest box dimension, less the value of skinnb, which defaults to 2.0.
So, there is a maximum value that is allowed.

There is (in general) no simple relation between "accuracy" and cutoff.
Using a switch may improve energy conservation in NVE simulations.
Using a larger cutoff value can in principle lead to better results, but
these might be negated if the slower speed with the larger cutoff led
one to running a shorter simulation.


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Received on Sun Sep 01 2019 - 13:30:01 PDT
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