GROMACS version: 2024.5 and 2023.2
GROMACS modification: No
I have a bilayer with a protein created from Charmm-GUI where I’m trying to run an energy minimization following the README from Charmm. After running the two initial commands:
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -r step5_charmm2gmx.pdb -p system.top -n index.ndx -maxwarn 1
gmx mdrun -rdd 3.0 -deffnm step6.0_minimization
the mdrun produces:
Program: gmx mdrun, version 2024.5
Source file: src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp (line 1330)
Function: void nb_free_energy_kernel(const t_nblist&, const gmx::ArrayRefWithPadding<const gmx::BasicVector >&, int, const interaction_const_t&, gmx::ArrayRef<const gmx::BasicVector >, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef, int, gmx::ArrayRef, t_nrnb*, gmx::ArrayRefWithPadding<gmx::BasicVector >, real (*)[3], gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) [with DataTypes = SimdDataTypes; KernelSoftcoreType softcoreType = KernelSoftcoreType::Beutler; bool scLambdasOrAlphasDiffer = false; bool elecInteractionTypeIsEwald = false; LJKernelType ljKernelType = LJKernelType::Cutoff; bool computeForces = true; rvec = float [3]]
Error in user input:
One or more excluded and perturbed atom pairs are beyond the Coulomb cut-off,
which is not allowed with reaction-field.
when running it on the 2024.5 version. Running the same commands for the same system on version 2023.2 seems to run fine and does not produce this. I am not sure why version 2023.2 seems to run fine but not 2024.5?
Thanks!