Re: [AMBER] setting up a MD simulation using AMBER

From: David A Case <>
Date: Wed, 15 Jul 2015 11:41:18 -0400

On Wed, Jul 15, 2015, Amber mail wrote:
> 1. CHARMM27 force field for proteins.

You need to learn about the chamber program or, (better, I think) the chamber
option in You will need to set the system up in some CHARMM-aware
program (CHARMM itself, NAMD, CHARMM-GUI, vmd(??)), then convert files to
Amber format.

> 2. Lengevin dynamics for all nonhydrogen atoms with a damping
> coefficient of 1ps^-1 was used in maintaining a constant temperature of
> 310K throughout the system.

I don't think this is available in Amber. We apply the Langevin thermostat
to all atoms, not just to a subset of atoms.

> 3. Constant pressure of 1 atm was maintained using a Nosé–Hoover
> Langevin piston with a period of 100 fs and damping timescale of 50 fs.

This barostat is not available in Amber.

...good luck...dac

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Received on Wed Jul 15 2015 - 09:00:03 PDT
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