You can present the data differently:
you have two windows at 0.78 nm giving different distribution.
That indicates these windows are not converged. Does not mean
that the others (0.80 nm) are converged :))
On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote:
Hi Xavier
Thanks for the reply. With respect to your answer of my first query.
What if you had two windows practically on top of each other, but one
was not supposed to be there. e.g A window with r0 of 0.80 nm and
centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm.
Gavin
XAvier Periole wrote:
On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote:
Hi All
I have generated several PMF curves for the one system using
umbrella
sampling. In the first part of the curve (barrier region) I use a
high
force constant with small intervals between the windows. The
latter part
of the curve I use a lower force constant with larger window
spacing.
Anyway I have a few issues that I need clarifying:
1 - Can you have too much overlap between windows?
no, there no such a thing of too much overlap :)) You could even put
two identical windows with same 100% overlap ... no problem.
2 - Does the distribution at each window have to centered around the
desired r0? (If not does this affect the free energy?)
The deviation of the distribution from the r0 is what dictates the
profile. The more away from the disired r0 the higher the free energy
of the system.
3- If you over sample one particular window, will it affect the
curve?
There is no such a thing of over sampling ... the only thing you can
have is not enough sampling.
Many thanks
GAvin
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