From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 22 2003 - 18:16:05 CDT
Hi,
NAMD does not associate any energies with forces due to IMD. VMD
calculates forces based on the most recent coordinates it received from
NAMD and sends these forces back to NAMD asynchronously. NAMD has no idea
what the potential form is. This has never really been a problem in
practice, although it does make the conjugate gradient minimizer go into
fits, since (unlike in dynamics) the line minimizer actually uses the
total energy to bracket a minimum.
It has been my personal opinion that VMD should send NAMD a set of
restraint points or other parameters and let NAMD calculate the exact
corresponding forces and energies at every step. VMD could even ship NAMD
a complete Tcl force proc at every update. While not provided by the IMD
protocol, something like this could be implemented entirely in Tcl on the
NAMD side since the Tcl interpreter can use sockets directly.
-Jim
On Wed, 22 Oct 2003, Marc Baaden wrote:
>
> Hi,
>
> I am interested in the IMD functionality implemented in NAMD.
> In particular the way in which forces that are sent from VMD
> via the IMD protocol are handled.
>
> In order for the system to be consistent, an additional force
> must generate/depend on a corresponding energy. How is this
> done in NAMD ?
>
> My guess would be that one has to keep the coordinates at the
> time when a force is applied in memory, and the displacement
> with respect to these coordinates times the force times -1 yields
> a corresponding energy difference.
> Is this the way NAMD treats additional forces sent via IMD/VMD ?
>
> In that way, handling of the forces is independent of the tool
> that was used to generate them and one does not need to know the
> underlying equation of eg tug, spring or pinch .. ??
>
> Thanks in advance,
> Marc Baaden
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.marc-baaden.de
> FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217
>
>
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