[gmx-users] free energy calculation and constraint distance?

bmmothan at ucalgary.ca bmmothan at ucalgary.ca
Fri Jul 13 23:48:33 CEST 2007

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 understand there is a pull code with different
options or it can be done with constraint distances.

Please correct me if my procedure is wrong: I want to constraint several
distances between the ligand and the receptor and then  increase that
distance to one where the ligand and receptor are completely separated.
For that, I would have to modify my topology where i define [ constraints
] for the distances i want to constrain between the ligand and the
receptor and input the bond length for state A(lamda=0) and state B
(lamda=1) for each.

will the distances defined move the whole ligand away from the receptor?
since am only defining several distances between ligand and receptor only.

or is it recommended to use the pull code?

Any directions is appreciated.


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