AMBER Archive (2008)

Subject: Re: AMBER: using Velocity-Verlet algorithm

From: David A. Case (
Date: Thu Jun 12 2008 - 11:09:49 CDT

On Thu, Jun 12, 2008, oguz gurbulak wrote:
> I'm trying to run Constant-pressure constant-temperature MD simulations of
> DMSO ( Dimethyl Sulfoxide )-H2 O mixture at ambient conditions to evaluate
> structural and dynamical properties. MD simulations will be carried out
> within the NPT ensemble at T ) 303 K and p ) 1 atm . I want to solve the
> equations of motion using the Velocity-Verlet algorithm with the time step
> of 1fs.

Amber effectively uses the velocity Verlet algorithm by default. Note that
with both a thermostat and barostat turned on, the term "velocity Verlet"
loses a lot of its meaning (since that was originally for NVE simulations).

> I would like to use OPLS/AA force field

Amber does not provide files that implement OPLS/AA. You might be able to
prepare an Amber-style parameter file with OPLS/AA DMSO parameters in it;
that is probably not a difficult task for someone familiar with the file
formats that Amber uses, but would be more work for someone new to the

...good luck....dac

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