On 2/1/13 6:07 PM, Sonia Aguilera wrote:
Hi!
I just finished a FE calculation using the BAR method. This is the plot of
my histogram.xvg file:
<http://gromacs.5086.n6.nabble.com/file/n5005095/Screenshot.png>
It is my understanding that data must be overlaped in order to get adequate
sampling (I have been following Justin Lemkul's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html).
However I have a few questions (First two must be really simple, but I just
have not been successful):
1. How can I plot the ∂H/∂λ values separately from the ΔH values? I have
been trying, but I'm not really an expert using xmgrace.
You will have to parse the .xvg file, either manually or with a script, in order
to separate the data sets.
2. I also tried to plot this data using gnuplot. However, this program does
not distinguishes between diferent leyends, as in the xmgrace plot. Is there
any way for plotting the this data using this program?
All Gromacs programs allow you to turn off XmGrace-specific formatting with
"-xvg none."
3. Comparing my plot with the one on the tutorial, something is wrong with
my sampling. I have been trying to understand Bennett's paper, but I have
not been successful. Can someone explain to me the meaning of the values in
each axis? How should I interpret this data? What can I do to improve my
sampling?
In a very basic sense, the result is a series of histograms of energy values
from neighboring lambda windows. You need continuity in sampling from lambda =
0 to lambda = 1 in order to establish a reliable value for deltaG. It seems
from your plot that you are only using a few lambda points, with large gaps
between 0.1, 0.5, and 0.9. You probably need more windows.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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