[gmx-users] Help with using g_bar

Warren Gallin wgallin at ualberta.ca
Wed Apr 6 19:05:41 CEST 2011

On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:

> 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.

foreign_lambda was set, hence all the ∆H curves.

I've attached the .mdp file for both directions of the simulation.

> 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.
> -Justin
>> Thanks,
>> Warren Gallin
>> ------------------------------------------------------------------------

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