On 7/3/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
Do you know or can you suggest some results based on the comparison of
the force constant in Umbrell Sampling? Any literature?
That would be lovely, but I've never seen such a thing. One could probably
write a book with all the test cases that would be required. My gut tells me
that you can't generalize too much in terms of pulling simulations - the
approach depends on what is being pulled (small molecule, peptide, large
protein), what the medium is (water, membrane, etc), and what the interacting
partner is (protein surface, ion channel, binding pocket).
As far as I understand when you use the same staring coordinates (from
the same pulling simulation) for windows but you just change the force
constant (e.g. from 500 to 2000 kJ/mol nm2) you should increase number
of windows (for f=2000) as smaller force constant will cover wider
neigboruring distances - that makes sense.
I am curious whether the final result will be the same? I guess with
stronger force it will converge faster but more windows are required.
is it the only one difference?
Without a systematic comparison, it's hard to say, but in theory if one samples
sufficiently and has good overlap between neighboring windows, the results
should converge to the same answer.
If someone knows of some applicable literature that has done such comparisons,
please post a reference. I'd love to see it. Most SMD and US methodology is
written with hand-waving explanations as to what the authors did and why it
worked, and I have a suspicion that most reviewers don't have a better idea so
they can't refute such claims.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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