Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation

From: Sally Pias <>
Date: Thu, 9 Jul 2020 19:27:40 -0600

Hi Andrea,

In my experience, these settings should be fine. It is probably a good idea
to use the zero surface tension, as you have, but to my knowledge this
approach has not been rigorously tested.The Monte Carlo barostat would
speed up the simulations but seems to skew the box dimensions faster than
the Berendsen barostat without a surface tension. You will also likely see
a moderate increase in bilayer thickness with the Monte Carlo barostat,
though I am not convinced the values we have seen are out of the range of
experimental measurements. The performance increase may be worth switching
barostats (giving an additional 50 ns for equilibration with the new
barostat). It is probably also best to use the zero surface tension because
box dimension changes can be dramatic on the microsecond timescale,
especially in lipid-only systems. However, an imposed surface tension is
not physically rigorous and may have some minor physical effects.


Sally Pias
New Mexico Tech

On Thu, Jul 9, 2020 at 3:32 AM Andrea Pasquadibisceglie <> wrote:

> Hi Sally,
> I used the default value (0.0 dyne/cm) for the surface tension
> parameter. Is that correct?
> The simulations will be one or two microseconds long, and the issue I am
> referring to is:
> /"a substantial skewing of the box vectors can occur over very long
> simulation timeframes."/
> Thank you,
> Andrea
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Received on Thu Jul 09 2020 - 18:30:05 PDT
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