[gmx-users] Help with using g_bar

[Warren Gallin]

   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

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