AMBER Archive (2004)

Subject: AMBER: Question for PMEMD users

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jan 20 2004 - 10:05:38 CST

Folks -
I am in the process of updating PMEMD for the amber 8 release. Current
plans are for it to still do core pme functionality, but in the fashion of
sander 8; ie., the outputs from standard pme md and minimizations will be
completely compatible. We have been considering for a while also adding
support for "calculating free energies via thermodynamic integration (icfe
option in mdin)". Supporting this in pmemd is nontrivial, so I wanted some
feedback from users as to whether anyone would actually use this stuff if I
do it. Please respond directly to me (rduke_at_email.unc.edu) instead of to
the amber reflector, just to cut down on unnecessary message traffic for
everyone. Also, if there is any other functionality that would be highly
desirable in pmemd 8, I am open to suggestions (but not making promises).
Thanks very much for your input!
Bob Duke

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