AMBER Archive (2002)

Subject: Re: external electric field/another try

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Nov 27 2002 - 17:27:32 CST

Dear Ionna
I'm not sure if this will help. I don't have a good answer for periodic
systems. If its a cluster the cleanest approach is to add a short
subroutine implementing Tieleman, Berendsen and Sansom's idea. simpler yet
but more approximate approach is to add some distant fixed charges.

If its a 2d periodic system e.g. membrane you can embed in a larger 3d
periodic (with vacuum above and below system), but there's a technical
problem, at least for amber. If you are interested in that application I
can try to go through the Tieleman paper and see if its feasable for an
amber modification
hope this is helpful
Tom Darden
 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
>
>