Matt,
Thank you very much for the clarification. None of my calculations have involved
combined insertion/deletion. I have always picked the state that has more atoms
for my
starting state, then mutated toward the state with fewer atoms. This means that
I don't
have to re-do recent simulations (hurray!) but I'm still not sure why some of
them give
the results they do (boo!).
If you want (on or off-list) to give some more particulars about what
exactly you're doing and how, I might be able to give some suggestions
for things to look at. (i.e., particular molecule(s) you're working
on, and maybe a pdb code/file or two, along with some lambda values,
simulation lengths, etc).
I am amazed what I have learned about free energy calculations from this list
and from
papers suggested on it (Michael Shirts' recent work in particular, even if I
don't need
as much accuracy and precision as he achieved). The documentation for most
packages that
support free energy simulations is almost criminally simple in its description
of the
process. When I first started investigating thermodynamic
perturbation/integration, it
seemed like it would be fairly straightforward to use. I thought maybe it would
increase
setup time by about 50% and simulation time tenfold. Now it seems like it's
practically
a discipline unto itself. Review articles and original papers from 10-15 years
ago also
made me think the process would be much simpler than it actually turns out to
be. Even
books from the last 5 years haven't given me nearly so much useful information
as
references and suggestions from this list have. There's a big gap between
getting
roughly plausible results and getting reliable quantitative information, and it
seems
that most published material I've seen never crosses that gap.
Agreed. I had pretty much the same experience when I started off
beginning about a year and a half ago, although I spent most of the
time figuring out stuff for myself for a while.
Michael Shirts and I and a couple others are hoping to put together a
"best practices" review paper for free energy calculations in the
relatively near future, as this seems to be something rather badly
needed.
David
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