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
simulation.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 24 2018 - 04:30:01 PDT
