[gmx-users] some questions about umbrella sampling

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Thu Dec 10 17:19:05 CET 2009

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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