From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Wed Dec 08 2010 - 17:57:40 CST
Dear ABF users,
1) I have divided the RC of my system to several windows as below in order to improve the sampling and I am running the ABF simulation for all individual windows simultaneously.
Window1:
Xi min=-16.5
Xi max=-13.5
Window2:
Xi min=-13.5
Xi max=-10.5
and so on. The bin size is 0.2 in all the windows. Then I concatenate the .dat files (NAMD 2.6) from individual windows to generate the total .dat file by adding these lines in configuration file and running a simulation with timestep =0 as posted on the website before.
abf outFile total.dat
abf inFiles {1.dat 2.dat ...}
I am wondering how the program does this. I mean for the total.dat file the values of A(xi) in all of the bins are the same as window1. For the other windows, it adds a value to all A(xi)s in each window which is different for different windows but the same for all bins in each window. I did not find any discussion about the method for concatenating on the website. I would really appreciate if any one could address me how I can learn about this.
2) I am also using "abf forceConst 10.0 " to confine the ion movement "channel ion" inside the channel. I know the force is supposed to act at just the boundaries (Xmin and Xmax). But, my boundaries in the windows above (I have 11 windows) are part of RC. So, my assumption is that this force is going to affect the PMF profile at least at the boundaries of my windows. Right? Does the program finally correct this? Or am I missing something here?
Many thanks,
Parisa
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