Subject: Electromagnetic waves within CHARMm

From: Greg Lakatos <[email-masked]>
Date: Tue, 19 Sep 2000 23:37:48 -0700 (PDT)

Hello,

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?

Thanks very much for the help.

- Greg Lakatos
([email-masked])

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From: Eugene Leitl <[email-masked]>
Date: Wed, 20 Sep 2000 01:15:53 -0700 (PDT)

> given the wavevector, polarization, amplitude, and frequency of the wave?

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.

---

From: Rick Venable <[email-masked]>
Date: Wed, 20 Sep 2000 10:29:56 -0400

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?

> 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
[email-masked]          |    \  /  |=|    position of the FDA; for that,
[email-masked]              \/   |=|    see   http://www.fda.gov  )