Oh, now that you say non-periodic the problem is much easier.
Yes, just add the force Berendsen talks about. It should be
simple to do by using the subroutine xconst in sander/runmd/force
as a model for adding a simple force to the whole Hamiltonian.
jim
On Wed, 27 Nov 2002, Ioana Cozmuta wrote:
>Hi amber users,
>
>I am trying to send this message again, maybe somebody will still have an
>idea and with the annotation that I do not want to use it for periodic
>systems.
>There's only one paper by Tieleman, Berendsen and Sansom that I've found
>in Biophysical Journal, 2001 on this subject and the thing they suggest to
>do is to add a term F_i=q_i*E to the forces on all atoms i (with E a
>constant field).
>
>Once again, I would appreciate anyone's opinion on this matter.
>
>Thanks,
>Ioana
>
>---------- Forwarded message ----------
>Date: Mon, 25 Nov 2002 15:18:38 -0800 (PST)
>From: Ioana Cozmuta <ioana_at_nas.nasa.gov>
>To: amber_at_heimdal.compchem.ucsf.edu
>Subject: external electric field
>
>Hi ambers',
>
>I was wondering if anyone has any experience in running calculations and
>also accounting for the presence of an external field. Has anyone tried to
>use amber with this kind of calculations? Is there anyone that can give
>advice on this: what is the best way to implement it, some tricks of the
>trade?
>
>Thanks in advance,
>Ioana
>
>
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Received on Wed Nov 27 2002 - 15:31:24 PST
