GROMACS version:2022
GROMACS modification: Yes/No
I am trying to perform simulation on my protein-ligand complex following Gromacs Protein-Ligand complex tutorial, during NVT equilibration using the command
"gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr "
i encountered an error
“Assertion failed:
Condition: ip.conctr.dA > 0
We should only have positive constraint lengths here”
How to solve this error ?
A user should never get an assertion failure. That has been fixed in 2022.4.
But you do have a constraint with length zero in the system. This is allowed and treated as a flexible constraint, but very likely this is not what you want. I don’t know how you generated your topology, but my guess is that your ligand has one or more constraints where the length is set to zero, which is incorrect.