Re: [AMBER] Langevin Dynamics on selected atoms?

From: Jose Borreguero <>
Date: Fri, 3 Jan 2014 10:46:07 -0500

> Correlation functions of what?
The incoherent structure factor I(Q,t) of the hydrogen atoms (the Fourier
transform of the dynamic self distribution function g(r-r0,t) )

>Why not just run NVE?
I am running a relatively small molecule in vacuum at T=200K, thus the
molecule behaves as a harmonic solid except for the methyl rotations. I
wanted to measure I(Q,t) for these rotations but the low-frequency harmonic
motions of the rest of the molecule degrade the signal coming from the
methyl rotations. Unfortunatley, running in the NVE at low T and in vacuum
preserves these harmonic motions.
The harmonic motions can be removed by including interactions with external
particles, either real (solvent) or ghost (Langevin dynamics). In
particular, if you use Langevin dynamics with damping coefficient w_0, you
will decorrelate any harmonic motions with frequencies under w_0, thus
cleaning the I(Q,t) signal. Also, the external interactions will affect the
methyl rotations weakly if they are applied only to non-hydrogen atoms. If
you "bombard" the hydrogens with ghost particles, you will also decorrelate
the methyl rotations.

On Fri, Jan 3, 2014 at 12:34 AM, Jason Swails <>wrote:

> 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?
> No.
> > 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
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Jan 03 2014 - 08:00:02 PST
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