Re: [AMBER] How is temperature in Amber MD simulations calculated?

From: Jason Swails <>
Date: Thu, 10 Jul 2014 13:53:30 -0700

On Thu, Jul 10, 2014 at 1:40 PM, Brian Radak <> wrote:

> The instantaneous temperature, to my knowledge, is just calculated as the
> average kinetic energy of all of the particles (using the masses and
> velocities) scaled by kB and the number of degrees of freedom. There are
> some minor tricks used to get the velocities from the leap frog scheme, so
> you will probably not be able to do this calculation by hand from the
> velocity output (same goes for the potential energy though).


It should be noted that there are TWO input temperatures, tempi and temp0.
> The first is only used when velocities are not read from inpcrd and defines
> the distribution from which random velocities are drawn. The second one is
> a thermostat parameter and only affects the force calculation and/or
> velocity updates.

A word of caution -- setting a target temperature does nothing if you don't
actually use any kind of temperature control (like Langevin dynamics or a

Specifically, you need to set ntt=1, 2, or 3 in order to have sander or
pmemd drive the temperature toward temp0. I suspect you may have set temp0
to a target temperature but you didn't set ntt (which defaults to 0, or


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 10 2014 - 14:00:02 PDT
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