[gmx-users] Help with using g_bar

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 6 18:58:49 CEST 2011

Warren Gallin wrote:
> 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?

A complete .mdp file would help.  I'm guessing you didn't set foreign_lambda for 
any of these simulations?  g_bar works by evaluating energies at native and 
foreign lambda values.

A tutorial is in the works (but not for this specific application; free energy 
simulations in general).  No promises on when it will be done, but hopefully 
very soon.


> Thanks,
> Warren Gallin
> ------------------------------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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