I am doing umbrella sampling to calculate energy profile of an drug
passing through a ion channel by GROMACS3.3.
why not gmx 4?
In order to get right result, I need to choose a reasonable force
constant in my simulation, right? I know that, a reasonable force
constant should produce enough "overlap" to reduce WHAM errors, But
I'm wondering "how much overlap" are reasonable overlap?Does there
any rules I can use to judge whether my "overlap" is enough?
I aim for 20%, but that's because I also conduct REMD-like exchanges.
To be sure, you can do twice as many (or otherwise increase the
overlap) and if the profile doesn't change then you had enough to
begin with. I realize that this isn't a fantastically efficient
solution, but I don't know of a better one.
My second question is that, how to choose "number of bins", when I
using g_wham command? Does it decided by the numbers of windows I
used? I found that, different numbers will produce slightly
different results (a difference of 0.5kcal/mol in my condition).
What does it mean? Does it mean that, my simulation is not enough?
It could mean a lot of things. Based on what you mention below, I
suspect that you are using too bins that are too small when the energy
changes. WHAM works with probability histograms, and so you need
enough counts per bin that if you were to run the entire simulation
again the difference would be a small fraction of the average.
the third question: I found someone say that, to get results in a
good quality, one must make sure that, "individual histograms should
look smooth". What does it mean? Does it mean that,the distribution
of the positions of the drug in one window should be "smooth"
Yes
or should opproximately be an Gauss distribution
No. They could easily be bimodal.
(I found that, whether it is smooth is decided by the number of
bins, if a very large number of bins is used, it is not smooth)?
See my comment above regarding probability histograms
The last question: if my simulation produced enough "overlap", can I
believe that, my simulation is "right" theoretically?
No. Your sampling within one or many or all umbrellas could still be
trapped -- hence the reason that I do equilibrium exchange. Consider
this:
|------ Sidechain A
|
---| <drug in umbrella N>
versus:
---| <drug in umbrella N>
|
|------ Sidechain A
Regular US does not offer an efficient mechanism for the sidechain A
to switch sides of the drug while the drug is restrained to a given
position when the drug is blocking the rotamerization of that
sidechain. Allowing the constituent ensembles to interconvert using
e.g. REMD alleviated this sampling deficiency.
Chris.
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