GROMACS version: 2020
GROMACS modification: No
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Dear gromacs users
Hello, I have a basic question about the gmx lie command.
To run the gmx lie, What I currently understand is I need Eqq, Elj, which stands for Coul-SR(A-B), LJ-SR(A-B) values from ligand-solvent md run
and ‘.edr’ file which is generated from the Protein-ligand md run, through .mdp containing energygrps term.
However, when I tried to run gmx lie, it seems they don’t get the ‘LJ and Coul of Protein-ligand’ from the ‘.edr’
######Below is my command and the result##########
gmx lie -f ie.edr -Elj -5.88157 -Eqq 48.1747 -ligand chain_b
Opened ie.edr as single precision energy file
Using the following energy terms:
LJ:
Coul:
Last energy frame read 100 time 1000.000
DGbind = -23.023 (-nan)
################
I generated '.edr’file through below command.
‘gmx grompp -f ie.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o ie.tpr
gmx mdrun -deffnm ie -rerun md_0_10.xtc -nb cpu’
I look forward to your guidance and suggestions.
Thank you
Lee