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 >> ------------------------------------------------------------------------ >
run.mdp
Description: Binary data
run_bar_l.mdp
Description: Binary data
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