From: Shen, Han (han.shen_at_bme.gatech.edu)
Date: Mon Feb 06 2012 - 11:03:44 CST
Dear All,
I tried to follow "Free Energy of Conformational Change Calculations" to calculate the free energy of dimer separation. During the simulation, I separate the dimer from 5A to 30A, and then move them back to 5A. The pmf file is as below.
pmf {
task = grow
time = 1 ps
print = 1 ps
}
pmf {
task = up ## move from 5A to 30A
time = 100 ps
}
pmf {
task = down ## move from 30A to 5A
time = 100 ps
}
}
However, the free energy at the beginning of "down" is not the same as the end of "up", looks like that it has been reset. Both the free energy of "down" and "up" keep growing during the task, which doesn't look like the real case. I am not sure if I did something wrong or this is not the proper method for my study. Is there a tutorial for this method? Hope someone can give me some suggestions! Thanks so much in advance!
-- Han Shen Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University
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