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                                            Yoik

Double and triple bonds not correctly recognized (Problem with reading smiles or potentials?)

I’ve also encountered this issue. Based on my analysis, there are likely two root causes. First, the output CIF and PDB files only describe the bonding information between atoms in...

Compilation with patched Gromacs-2025-2 (and -1) gives error

replace all "cmd" to "plumed_->cmd" in this file "gromacs-2025.2/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp" example⬇️ try { // setup: these instructions in the original patch are BEFORE do_force() // now this is called within do_force(),...