Dear All:
I am doing umbrella sampling to calculate energy profile of an drug
passing through a ion channel by GROMACS3.3.
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?
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?
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" or should
opproximately be an Gauss distribution(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)?
The last question: if my simulation produced enough "overlap", can I
believe that, my simulation is "right" theoretically?
Thanks in advance!!!
R-X Gu
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