[gmx-users] Umbrella sampling
gmelaugh01 at qub.ac.uk
Thu Mar 31 11:53:49 CEST 2011
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?
2 - Does the distribution at each window have to centered around the
desired r0? (If not does this affect the free energy?)
3- If you over sample one particular window, will it affect the curve?
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