Re: [AMBER] How can I solve the high RMS problem?

From: David A Case <>
Date: Sun, 29 Nov 2020 13:45:07 -0500

On Thu, Nov 19, 2020, 변진영 wrote:
>As I know, in minimization step, the RMS values which is printed out
>in mdout file are lower than zero when the energy minimization step is
>finished properly.

This is not correct: by its definition, a root-mean-square result can
never be less than zero.

> 999980 -8.8296E+05 1.2437E+01 8.0883E+03 H1 13451

You still have fairly large gradients, even after a million(!) steps of
minimization. Something looks wrong, and only a few thousand steps of
minimization should be required.

Be sure that "standard" runs (without TI, i.e. at one or both of the
endpoints) work correctly. One would generally carefully equilibrate
one of the endpoints before embarking on free energy simulations.


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Received on Sun Nov 29 2020 - 11:00:04 PST
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