[gmx-users] gromacs result

[Mark Abraham]

mahbubeh zarrabi wrote:
> Dear all
> I have 3 complexes of docking.(one receptor with 3
> different ligands).I studied MD of 3 complexes in 15
> ns by gromacs.how can i compare binding energy and
> affinity of 3 ligands with receptor.(how can i
> analysis gromacs result)

Shouldn't you have asked this question before designing your
simulations? :-) You can't measure binding affinity without taking a
difference between "before" and "after", which you don't seem to have.
You probably need to look at literature on thermodynamic integration, or
some such.

Mark