YASARA does not contain a built-in ability for umbrela sampling/WHAM simulations. I have built such scripts, which perform the simulation and generate the files needed as input for the WHAM program (http://membrane.urmc.rochester.edu/?page_id=126). I will distribute them on request. Drop me a line at pedros_at_ufp_dot_edu_pt
I only ask to be mentioned in the "Acknowledgments" section of any papers where this script is used.
After considerable debugging and improvement I now feel confident enough in the smooth operation of the macro to release it into the world. Happy sampling!
Thank you very much for sharing the script. I have one questions, concerning variables. Could you please explain what should be here (in direction):
# string to append to the name of the simulation, intended to facilitate the distinction of the files
# produced from different simulations based on the same scene. ideally, this string should NOT contain
# any spaces
direction=''
If understand correctly direction is defined by anchor atoms?
Thank you in advance, Natalia Kulik
Natalia Kulik The variable I called "direction" is simply a word (or longer string) taht is added to the filenames of the results files to allow the user to run different WHAM simulations from the same starting scene without danger of using files from previous runs.
@ For example, imagine your scene is called "isomerase_with_inhibitor.sce" and you want to run different WHAM simulations (for example, by choosing different spring constants, or larger equilibraion periods, etc.) you could set
direction = 'stiff_spring'
and the result files would then have names like "isomerase_with_inhibitor_stif_spring*.* "
Running a new WHAm simulation (with different parameters, for example) and setting
direction= 'longer_sampling_time'
would generate files with names like "isomerase_with_inhibitor_longer_sampling_time*.* "
etc.
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