Removing the normal modes not including methyl rotations sounds like a
great idea! On the other hand, I think the FFT filter would be tricky when
trying to remove harmonic motions with frequencies of the same order as the
transition rate for the methyl rotations.
On Fri, Jan 3, 2014 at 10:52 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Dear Jose
>
> I think you are technically correct, but the ensemble that you create by
> using a differential langevin bath is weird at best. I think one 'could'
> figure it out, but it would resemble no known experiment I cam imagine.
> If you truly believe that the 'rest' of the system is harmonic, you
> could just run NVE for everyone and then do onw of two things
>
> 1. project out the normal modes for the modes that do not include methyl
> rotations. If you can get the normal modes, this should work.
> 2. simply apply a filter to your FFT, which I believe is exactly the
> same as applying a damping term to the dynamics.
>
> a.
>
> On 1/3/14 10:46 AM, Jose Borreguero wrote:
> >> 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 <jason.swails.gmail.com
> >wrote:
> >
> >> On Thu, Jan 2, 2014 at 3:21 PM, Jose Borreguero <borreguero.gmail.com
> >>> 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Fri Jan 03 2014 - 08:30:03 PST
