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

From: ANDREA PASQUADIBISCEGLIE <andrea.pasquadibisceglie.uniroma3.it>
Date: Mon, 6 Jul 2020 15:49:36 +0000

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 http://www.mdtutorials.com/gmx/membrane_protein/07_equil2.html).
Do you think I should change any of these parameters? Any advice is welcome!

Thank you in advance,

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Received on Mon Jul 06 2020 - 09:00:04 PDT
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