Re: [AMBER] constant-pressure equilibration with a water droplet

From: David A Case <>
Date: Mon, 29 Apr 2019 14:06:09 -0400

On Mon, Apr 29, 2019, Anthony Bogetti wrote:
>I am trying to equilibrate my system of a solute molecule in a water
>droplet. I have successfully performed a minimization and a
>constant-volume equilibration. How can I perform a constant-pressure
>equilibration? I get an error saying that NTB cannot be zero when using
>NTP > 0. What is best practice in terms of equilibrating with a water
>droplet? Are there any example input scripts I could see?

Just to expand a bit on Carlos' answer:

Basically, Amber is not set up to perform "real" simulations in a water
droplet. The surface tension of water is great enough that you can run
a simulation of a solute/droplet for a fair while, and only a few waters
will "evaporate", and fly off into space.

But eventually, more and more water molecules will fly away. Even
before that happens, the properties of the water droplet/aerosol may not
be a very good match for any experimental condition: the water models
available in Amber are pretty much exclusively designed to work in
periodic simulations, not for droplets.

It is possible, in principle, to simulate a mixed-phase (periodic)
system, in which droplets co-exist with water vapor. But you'd want to
do a literature search to see how something like this could actually be
carried out.

Bottom line is that Amber is very heavily tilted towards periodic
simulations: we don't support things like reaction fields or stochastic
boundaries (as does, for example, CHARMM) that would help with
non-periodic simulations.

...good luck....dac

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Received on Mon Apr 29 2019 - 11:30:02 PDT
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