GROMACS version: 2020.1
GROMACS modification: Yes/No
Hi , there
I wanted to pull a ligand out of the protein-ligand complex in the z-axis determined by fast pulling ligand method. But encountered an error during the run like this:
ERROR 1 [file md.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.
Pull group natoms pbc atom distance at start reference at t=0
1 4516 2258
2 82 4557 0.056 nm 0.056 nm
Estimate for the relative computational load of the PME mesh part: 0.31
This run will generate roughly 11 Mb of data
My command to run md is as follows:
gmx_mpi_d grompp -f md.mdp -r npt.gro -c npt.gro -t npt.cpt -p top.top -o md.tpr
Previously, I was running NVT and NPT successfully. Here are the options for the md.mdp file.
The water box designed for the complex is as follows
gmx editconf -bt triclinic -c -d 0.8 -f rec.pdb -o rec1.pdb
gmx editconf -box 8.316 8.316 12.380 -center 3.808 3.468 3.040 -f rec1.pdb -o rec1.pdb
gmx solvate -cp rec1.pdb -cs spc216.gro -p top.top -o rec1.pdb
I still don’t understand where the error happened. Can you explain and give a solution for me?.
Thanks!