Welcome to the world of science...
But I thought exactly the same as you do and therefore give a +1 to your
mail...:)
Regards
(BTW: Sorry, for this needless spam...)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
[EMAIL PROTECTED] wrote:
Sorry about all of the confusion. Basically, the answer to this
depends on what exactly you're doing. (I should really write all of
this up in a tutorial soon). The way I think about it is that there
are two fundamental principles you need to keep in mind, and you can
do it any way you can cook up as long as you follow these two:
(1) Always use soft core when modifying vdW interactions
(2) Never leave charges on atoms for which you are turning off the vdW
interactions
The corollary is that you should generally not change charges and LJ
interactions at the same time, but this is more for efficiency reasons
than anything else.
So, if you can cook up a way to do what you want that doesn't violate
principles (1) or (2) and only involves two steps, great. For my
purposes, I'm doing absolute binding free energy calculations where I
don't mutate one thing into something else, so I can always do this --
I'm just disappearing atoms, so I first turn off teh charges, and then
second turn off the LJ interactions.
More generally, I suppose if you can think of a way to do the
transformation you want that only involves either (a) inserting atoms,
or (b) deleting atoms, but not both, you can do it in two steps. If it
only involves insertion, you first modify the LJ interactions to
"appear" some dummy atoms, and then turn on their charges. If it only
involves deletion, you first turn off the charges, then you turn off
the LJ interactions. If it involves both insertions and deletions,
maybe there is a way to do it in only two steps, but it isn't obvious
to me.
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!).
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.
Again, thank you very much for your patient support and education that goes
hand in hand
with your excellent simulation software.
Matt Ernst
Washington State University
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