I am trying to use g_bar to derive a PMF curve from non-equilibrium trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. I am using the end-to-end distance of a peptide as the co-ordinate of interest. After doing a long simulation of the peptide, I selected the frames with the longest and shortest end-to-end distances, imposed a restraint on the end-to-end distance by adding a type 10 bond centered on the end-toend distance in the farme with a large force constant to the topology, and then ran a simulation to generate an ensemble of conformations with the end-to-end distances restrained at the longest and shortest distances. I then selected 5 frames from each of those two simulations and used those as the starting conformations for 20 ps simulations with free_energy set to yes with the end-to-end distance changing linearly with lambda between the two distances, with 11 equally spaced foreign_lambda values, from 0 to 1.0. I got what I thought would be tyhe expected dhdl files (see two attached files, one for short-to-long and the other for long-to-short). However, when I invoke g_bar with these ten files as input I get no PMF, the free energy difference between the longest and shortest distances is printed out as zero, and I get a histogram file with extensive overlap. So, I must be making a mistake in either choosing the simulation parameters for the non-equilibrium trajectories or I am misunderstanding what g_bar is supposed to do, or 5 simulations in each direction is not enough to get any kind of output. Note, I realize that I will need to run many more non-equilibrium runs to get a reliable analysis, but I am just trying to run a minimal test to be sure that I am not off on the wrong track. Could someone suggest where I am going wrong, and even better where I might find some documentation of the operational use of g_bar? Thanks, Warren Gallin
Long-to-short dhdl file.pdf
Description: Adobe PDF document
Short-to-long dhdl file.pdf
Description: Adobe PDF document
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