GMX lie usage

User discussions
1

GROMACS version: 2020.6
GROMACS modification: No

Hi all, this question is similar to another question posted here which hasn’t had any replies: The input for gmx lie?

In summary, gmx lie doesn’t seem to find the ligand-protein interaction energy terms in the specified EDR file. What exactly does gmx lie look for? I’ve specified energygrps = LIG Protein and used -ligand LIG when calling gmx lie, but as in the other post:

Using the following energy terms:
LJ:
Coul:

It doesn’t seem to find any energy terms

2

Hi,
I have not used it recently, but to utilize gmx_lie, two simulations are required: one with the ligand bound to the protein and one with the ligand in water. Both need to utilize energygrps such that Coul-SR(A-B), LJ-SR(A-B), terms are written to the eneryg file. Values from the molecule-in-water simulation are necessary for supplying suitable values for -Elj and -Eqq.
Is it what you did?
\Alessandra