Re: [AMBER] Langevin Dynamics on selected atoms?

From: Jason Swails <>
Date: Fri, 3 Jan 2014 00:34:14 -0500

On Thu, Jan 2, 2014 at 3:21 PM, Jose Borreguero <>wrote:

> Dear AMBER users,
> Is it possible to apply the Langevin dynamics a subset of the atoms?


> I need
> to calculate correlation functions for the hydrogens of my system,

Correlation functions of what? Bond vectors? I can't imagine any
measurements you would make in which Langevin dynamics targeted to a subset
of the atoms would not impact their correlation functions.

and it
> would be handy to apply Langeving dynamics only to the heavy atoms so that
> the correlation functions are unnafected by the addition of the thermal
> bath.

Why not just run NVE? For a properly equilibrated simulation it should be
equivalent to an NVT ensemble as long as the settings were optimized for
good energy conservation (constraint tolerance, etc.). The upside is that
you can compute temporal properties from an NVE simulation (which seems
like it may be of interest to you).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 02 2014 - 22:00:02 PST
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