abf integrate on two dimensional pmf

From: Nadeem A. Vellore (vnadeem_at_gmail.com)
Date: Mon Oct 07 2013 - 21:25:11 CDT

Dear NAMD users,

I am trying to use the ABF with two variables (two-dimensional) for my
system and I have some trouble in collating the data.

1. I ran the two variable combinations using discrete windows. (var-1 and 2
divided into 5 windows : 25 windows in total)
2. Using the normal combining method I created the *.grad and *.count file
(with inputPrefix command in abf.in file and integrated by running for 0
3. the abf_integrate code was then used for creating the PMF file using the
default values
./abf_integrate comb_5ns.grad
./abf_integrate comb_6ns.grad
This produced the *pmf, *histo, *est and *dev file.

Everytime I re-run this on the same grad, I get a different PMF file. I am
doing something wrong.
Also, looking at the time-based PMF evolution, I see disconnection between
the first and second timescale data (meaning 5th and 6th). This is
meaningless at the moment, as I am not able to reproduce the PMF profile
for a given traj.

Can you please shed some light on this.


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