Re: [AMBER] Use of Amber12 and 14 on the same simulation

From: David A Case <>
Date: Thu, 24 May 2018 07:28:45 -0400

On Wed, May 23, 2018, JoAnne Babula wrote:
> I have two questions regarding the use of Amber12 and 14.
> 1. I have used Amber12 to generate from steps minimization, heat, density,
> and equilibrium, but then run the production steps on Amber14. Are these
> results still reliable?

They should be: for standard molecular dynamics, our codes have been
backwards compatible for about 20 years.

> 2. I have run simulations on two very similar protein structures, one on
> Amber12 and the other on Amber14. Are the results comparable between the
> two simulations?

Same as above. If you really want to check, download AmberTools18, and
use sander to run a short simulation (say 20 steps even, printing every
step), and compare to your Amber12/14 results.

Be sure to read the comments about round-off errors and trajectory
divergence on p. 24 of the Amber 2018 Reference Manual: it is not
generally possible to exactly reproduce the details of an individual


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Received on Thu May 24 2018 - 04:30:01 PDT
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