From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Tue Feb 01 2011 - 10:27:43 CST
Dear NAMD experts,
I am performing ABF calculations to capture the ion movement along a channel.
I have improved the sampling in some of the windows by dividing the whole RC to several windows, however, there is still a big difference in the number of samples at two ends of the window in some cases even after a long simulation time (20 ns). I am wondering what may cause this and is there any other solution to improve and smoothen sampling? I know increasing the current number of windows may help, but any thing else I can try? The position of the ion is already within the each window.
I have always seen people discuss this issue in the mailing list. I am wondering if there is any criteria to estimate the quality of the sampling? How do I know my sampling is good? If there is a huge difference in the number of samples in different areas (between 10k to 150k) or even more in one window but the force has converged (the pmf profile is not changing anymore), are the results acceptable?
Also, in NAMD 2.6 the history file of the system is reported and there is always access to the force and free energy (PMF profile) of the system at different time steps for different bins, however, in NAMD 2.7 (colvars), only the final information of force and free energy is reported in .pmf file unless you just copy your data manually during the simulation. I am wondering if there is any way to have these data at different time steps. This is really necessary for my system.
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