From: Krishnan, Marimuthu (krishnanm_at_ornl.gov)
Date: Thu Dec 17 2009 - 21:55:59 CST
I have a naive question about ABF simulations using NAMD. I would appreciate if ABF/NAMD experts could help me understand it.
I have performed a sequence of five 5-ns ABF runs. An equilibrated configuration sampled from a 300K-MD simulation was used as the starting structure for the first run.
For the next four ABF runs, the starting structures and initial velocities were taken from the final structures/velocities obtained from the preceding runs (the PMF
calculated from the preceding 5-ns run will not be considered/included (for the averaging purposes) in the present run). At the end, I have a set of five PMF profiles.
Is it meaningful to consider this set as an ensemble and to compute the average PMF profile out of it? Will the average PMF thus obtained be different (significantly or slightly) from that obtained from a set of 5 independent (each starting from MD-sampled random configurations and random velocities obtained from MB distribution) 5ns ABF runs? I am concerned about it for the following reason: if the starting structure of an ABF run was taken from the preceding ABF run, then the "influence" of the average force obtained from the preceding run would be present (implicitly) in the current ABF run. Is my understanding correct? Any expert advice would be greatly appreciated.
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