From: Patrick Yee (pyee_at_nd.edu)
Date: Sat Mar 27 2010 - 14:42:18 CDT
Hi NAMD users,
My question is about the data file generated using the ABF method. I
tried running two simulations, one as the NaCl tutorial and one as a
methane-methane simulation in water, to find the PMF's of both
systems. My results come out with great accuracy, but each simulation
has a high displacement from expected values. For example, the PMF for
the Na-Cl ion pair was calculated to be about 12 kcal/mol high for
each value, but after translating my data to a known value, results
looked fine. Is the displacement on expected results considered normal
behavior for using the ABF method or is there a problem with them?
Please let me know if you need any other parameters than those
included below.
After equilibrating the systems, I ran an NVE simulation with ABF parameters:
abf coordinate distance
abf abf1 1
abf abf2 2
abf ximin 0.05
abf ximax 14.95
abf dxi 0.1
abf fullsamples 4000
abf forceconst 10.0
writexifreq 10000
Energy in the ABF simulations was fairly constant and rigidbonds on
water molecules was not used.
Thank you very much!
Patrick
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