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Date: Wed, 20 Sep 2000 10:29:56 -0400
From: Rick Venable <rvenable "-at-" gandalf.cber.nih.gov>
To: Eugene Leitl <eugene.leitl%!at!%lrz.uni-muenchen.de>
cc: Greg Lakatos <greg:~at~:fjohn.stanford.edu>, chemistry:~at~:ccl.net
Subject: Re: CCL:Electromagnetic waves within CHARMm
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Greg Lakatos writes:
> Does anyone know if it is possible to have CHARMm simulate the
> effects of an EM wave interacting with a macromolecule?  In
> particular, is there a way to get CHARMm to compute the Lorentz
> force acting on an atom given the wavevector, polarization,
> amplitude, and frequency of the wave?

On Wed, 20 Sep 2000, Eugene Leitl wrote:
> I'm also interested in an answer to this, with an angle on NEMS (nano
> electro mechanical systems) utilizing optics and generally operating
> in a high energy density dissipation regime.

There is an addition to CHARMM (academic), but perhaps not in CHARMMm
(commercial) yet, named PULL described in cons.doc as follows:


[SYNTAX External Forces]

PULL { FORCe  <real>  }  XDIR <real> YDIR <real> ZDIR <real> [PERIod <real>]
     { EFIEld <real>  }
     { OFF            }
     { LIST           }
                         [WEIGht] atom-selection  


  A force will be applied in the specified direction on the selected
atoms  either as a constant:

  FORCe <value> specified in picoNewtons (pN)

or oscillating in time: 

  FORCe*COS(TWOPI*TIME/PERIod), FORCe <pN> PERIod <ps>

time is counted from the start of the dynamcis run.

  The force due to an electrical EFIEld (V/m) (possibly also
oscillating) may also be specified, in which case partial charges are
taken from the psf and used to calculate the force.

If WEIGht is specified the forces are multiplied by the wmain array.

Each invocation of this command adds a set of forces to the previously
defined set. 

PULL OFF turns off all these forces.
PULL LIST produces a listing. 

NB! Forces defined by PULL will move atoms in the specified direction,
which is opposite to that listed by the forces from the COOR FORCE
command.


--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
Rick_Venable $#at#$ nih.gov          |    \  /  |=|    position of the FDA; for that,
rvenable&$at$&speakeasy.org              \/   |=|    see   http://www.fda.gov  )