Re: [AMBER] How long should a NPT equilibrium take in QM/MM MD?

From: David Case <>
Date: Mon, 12 Nov 2018 22:16:48 +0000

On Mon, Nov 12, 2018, Meng Wu wrote:
> I'm trying to run a QM/MM umbrella sampling with amber.
> In the AMBER Advanced Tutorial 17 for umbrella sampling, the author
> first run a 2000 step minization then a 50ps NPT equilibration before
> production run.
> But my QM region include 80 atoms, 50ps NPT equilibration would cost
> me a long time if I use DFT method. So in a attempt I make, I only run
> a 1ps NPT equilibration with PM6DH+. Although I got what I want, but I
> do not know if I'm making mistake shorten the NPT run.

One key aspect of the NPT equilibration is to get a good density, so you
can monitor whether that has converged.

Another idea, that depends somewhat on the chemistry of your QM region:
put restraints on that region (with ntr=1), and run a pure MM NPT
equilibration. The QM region won't much (much), so deficiencies in the
MM description of it won't matter. You can then afford many nanoseconds
to get the MM region well-equilibrated.

After that, go back to QM/MM, removing the restraints.

...good luck....dac

AMBER mailing list
Received on Mon Nov 12 2018 - 14:30:03 PST
Custom Search