From: Marc Baaden (baaden_at_smplinux.de)
Date: Wed Oct 22 2003 - 16:36:35 CDT
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,
-- 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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