Some questions on the Deca-Alanine ABF tutorial

From: sunyeping (
Date: Mon May 16 2016 - 04:19:33 CDT

Dear all, I am studying the Deca-Alanine ABF tourial and ABF method. I have finished the 5 ns run of the tutorial but I have several questions on the analysis of the results. In the tutorial the figure 1 in page 10 gives the results of the potential (delta A(ξ))as a function of the distance (ξ).The range of the delta A(ξ)is from around -4 to 23 kcal/mol. The tourial says that convergence usually occurs within 5 ns and one of the criteria of convergence is that the pmf does not vary any more. It seems that we should exam the change of pmf against time to judge wether the simulation has converged. Is there a output file that gives the pmf vs time result? In my output pmf files, the delta A(ξ)ranges from about 0.2 to 39 kcal/mol, which is different from the tutorial. Is this OK? Another question is, in the figure 1 in the tourial, the inset shows the number of samples at each distance. How is the number of samples counted? Is it counted from the traj files? However, there are only 10000 frames in the traj file, while the number of samples in the inset figure are more than 1×105 at each distance. Where does these numbers come from?  The tutorial claims that the unfolding of deca-alaline is reversible and the different conformational states of the peptide chain are visited frequently. However, in my simulation, the unfolded peptide revert to the helix only in the last frame? Is this correct? The NAMD user's guide says that reconstructing multidemensional free energy surface requires abf_integrate command. But I cannot find it in the NAMD binary packages. where is this command implemented? Best regards.

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