POLL: free energy of conformational change

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Dec 10 2008 - 10:25:14 CST

Hi everyone,
Using this list to poll NAMD users is rather unusual, but I hope this
can be useful.

The question applies to those of you who have used (or considered
using) the "conformational free energy" function: how did you (intend
to) use it, for what purpose?
[I am talking about the function documented here:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html]

The reason for asking is that the interface design seems to be unclear
to some users, as indicated by numerous messages to this list, and
most of its functionality is available from various other parts of
NAMD (SMD, TclForces and TclBC, harmonic "constraints", ABF, and the
upcoming collective variable module). I suspect that the needs of
users could be better served by improving those other NAMD functions.

Since there might be many replies, I would appreciate if you reply to
this message _off-list_. I will collect your answers and send a
summary to the list, and discuss it, if needed, with NAMD developers.

Best,
Jerome

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