I bet, this topic has been discussed on the list multiple times before.
Numerical Integration is the keyword here and be aware of the problems
in calculating the total error from the single errors (look into Shirts
papers).
I suggest to inform yourself intensively about free energy calculation
methods, their pros and cons in general.
Using a tutorial is not the only thing to do, to compute meaningful free
energies.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Li Qiang wrote:
Dear all,
Can anybody tell me how to calculate the free energy difference after
running simulation with lamda(0, 0.1,...1)?
I am following the tutorial on wiki, but i have no idea about the
details to do the "data analysis".
any software can do it? and any reference for the instruction? I am new
here.
thanks a lot
Qiang
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