ABF with z-coord

From: Ugur Akgun (ugur_iowa_at_hotmail.com)
Date: Fri Nov 24 2006 - 20:31:06 CST

Dear all;
I am trying to run ABF to get energy profiles of a channel, I am getting
some inconsistent results, although the ligand moves along the channel the
PMF value I got from ABF keeps increasing. But in the energy landscape there
are peaks, and minimas.
I have selected 10-15A windows to run at a time, can this be a problem? Has
anyone faced this problem before?

I pasted the abf parameters I use:

Thank you

abf coordinate zCoord

abf abf1 {270 2550 4070}
abf abf2 {1 2 3 4}

abf dxi 0.1
abf xiMin -12.0
abf xiMax -3.0
abf forceconst 10.0
abf applyBias yes
abf fullSamples 500
abf outputfreq 5
abf writexifreq 10
abf dSmooth 0.1

abf outFile output_abf.dat

abf inFiles {}
abf distFile output_abf.dist
abf historyFile output_abf.history
run 5000000

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