Hello,
What I want to do is calculate the free energy difference of pulling the
ligand away from the receptor. I want to do it using theromdynamic
intergration using the Lamda 0/1 stuff. I am just not clear of the
procedure of how to do it.
I want to constraint several distances between the ligan
Sorry, I really didn't get, what your goal is and what, in fact, you
really want to do.
For free energy calculations, you can
- either do Thermodynamic integration (the lambda 0/1 stuff)
- or pulling (force probe) and afterwards use Jarzynskis theorem
- or umbrella sampling together with WHAM (i
Hello Gromacs users,
I am trying to do a free energy calculation, which I have never done
before. I have read the manual and the tutorial on the wiki but there is
still some issues not clear to me.
I am trying to calculate free energy difference of pulling the ligand from
a beta-sheet receptor. I
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