While trying to run the MD simulation with the CHARMM-GUI input file, I encounter such an error during the equilibration phase. How to overcome this?
gmx mdrun -v -deffnm ${istep}
Program: gmx mdrun, version 2023-Homebrew
Source file: src/gromacs/mdlib/sim_util.cpp (line 554)
Function: void checkPotentialEnergyValidity(int64_t, const gmx_enerdata_t&, const t_inputrec&)
Internal error (bug):
Step 0: The total potential energy is 1.03605e+19, which is extremely high.
The LJ and electrostatic contributions to the energy are 1.03605e+19 and
-2.96596e+06, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
Try a different itp generating servers i.e., swissParam, ligpargen, for your ligand and perform energy minimization for protein.
Other viz you may try Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...
Hello,
Try increasing the minimization steps, maybe your system needs more time reaching a lower energy state or maybe it got stuck at a high energy conformation when minimization steps ended.
Best,
Aysima
Check for overlapping atoms, suddenly there may be molecules very close to the ligand.
You can list what is next to the ligand using pymol.
selec byres all within 4 of resn LIG
You can always ask your GROMACS-related questions (only) on the GROMACS forum :
https://gromacs.bioexcel.eu/
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