My bad, I red to quick and though you had three windows ...
you should follow Justin's advice.
On Mar 31, 2011, at 2:20 PM, Gavin Melaugh wrote:
Thanks Justin for the reply
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Sorry I am not sure that I follow. Will the window with r0 =0.80
giving
the distribution centred around 0.78nm not drive my free energy
profile
up. If I remove this window prior to running g_wham the free
energy goes
down. Should I increase the force constant so that the mean of the
window is 0.80nm (bearing in mind that this is near the barrier
region).
If you have an incomplete or otherwise discontinuous free energy
profile, then you won't get a correct result, but it's not simply due
to "oversampling" one region. It's that the "oversampling" results
in
"undersampling" another region. Increasing the force constant for
the
window centered around 0.80 nm should work.
-Justin
Gavin
XAvier Periole wrote:
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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