concatenate pmf files in colvars

From: Parisa Akhski (
Date: Sat Jan 01 2011 - 12:23:06 CST


I have been using NAMD 2.6 to get the PMF for ion movement in a channel using several windows for the whole RC. I used
abf inFiles {1.dat 2.dat ...} in order to concatenate them at the end. I also used 2004 ABF paper to do this manually using the force values in .dat file and I got the same curve for PMF.

Now, I want to do the same thing using NAMD 2.7b3.

First, in .pmf files there is no force reported (there is just free energy values). Where I can get the force to calculate free energy at different bins and also concatenate them?

Second, If I want to use abf inFiles {1.pmf 2.pmf ...} to concatenate the pmf files, how should I use it? I used it as a part of abf section in colvar configuration file, but the program did not recognize it.

Thanks for your comments in advance,

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