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. 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? 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? Thank you in advance, Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-histogram-results-tp5005095.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
