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

From: Sally Pias <>
Date: Tue, 7 Jul 2020 21:16:56 -0600

Hi Andrea,

It is likely that these settings are fine. What surface tension value did
you set? Also, how long are you planning to run the simulation?

Which issues are you concerned about for long simulations? I did not find
that information on the linked page.


Sally Pias
New Mexico Tech

On Mon, Jul 6, 2020 at 9:49 AM ANDREA PASQUADIBISCEGLIE <> wrote:

> Dear all,
> I'm trying to understand which barostat and thermostat I should use to
> correctly simulate the binding of a ligand to a membrane protein inserted
> in a lipid bilayer.
> I built the system using CHARMM-GUI (CHARMM36m as force field), and as
> suggested in the Amber tutorial "An Amber Lipid Force Field Tutorial:
> Lipid14 Edition", I'm using the Langevin thermostat and the Berendsen
> barostat. However, I changed the pressure coupling to semi-isotropic,
> keeping constant the surface tension in the xy plane (csurften = 3), in
> order to avoid issues for long simulations (as suggested in GROMACS
> tutorial
> Do you think I should change any of these parameters? Any advice is
> welcome!
> Thank you in advance,
> Andrea
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Received on Tue Jul 07 2020 - 20:30:04 PDT
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