Warren Gallin wrote:
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.
OK, you've got a lot going on here:
init_lambda = 1
delta_lambda = -.0001
free_energy = yes
foreign_lambda = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
You're changing lambda as a function of time, and assigning a value of 1 to both
foreign and native lambda. More reliable settings have been discussed within
the last few days, i.e.:
http://lists.gromacs.org/pipermail/gmx-users/2011-March/059694.html
So I would suggest you turn off the slow growth setting (since I am not sure how
it will affect the BAR results, and because it's error-prone), and if that
doesn't fix it, split the transformation into a few separate simulations at
defined intervals of native lambda and foreign lambda (such that they don't
overlap, either).
-Justin
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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