This repository hosts auxiliary files to the Supporting Information of the following paper:

Gabriel Oanca, Florian van der Ent, Johan Åqvist, Efficient Empirical Valence Bond Simulations with GROMACS, Journal of Chemical Theory and Computation, 2023, doi: 10.1021/acs.jctc.3c00714

Inside the folder of each system, you will find the g09/ folder containing the Gaussian09 jobs and the maketop/ folder where we built the topologies. Inside maketop/, ffld_server parameters (.ffld files) and RESP charges (.ac files) will serve as input to ffld2gmx.py tool which generates GROMACS parameters in OPLS-AA format (.opls files). These .opls files, together with qmatoms.dat and topol.top topology created by GROMACS will serve as input for gmx4evb.py tool to generate the topologies (inside topologies/ folder) necessary for an EVB simulation with GROMACS.

qmatoms.dat file is structured as follows:

[atoms] directive contain the EVB atoms ('1' on the last column) as well as non-EVB atoms ('2' on the last column) involved in torsions, LJ14 and Coulomb-14 interactions with the EVB atoms. The columns are:

#pdb index, atom types (RS), charges (RS), atom types (PS), charges (PS), dummy types, EVB or non-EVB (1 or 2)

[soft-core] directive contains the soft repulsion parameter for atoms involved in breaking or forming bonds and/or angles. The soft repulsion interaction between two atoms, say i and j, has the form: A_ij * exp(-beta_ij * r_ij), where A_ij = A_i * A_j and beta_ij = sqrt(beta_i * beta_j). The coumns are:

#pdb index, A, beta

[bonds] directive will usually contain the Morse parameters for breaking or forming bonds. A Morse potential has the following expression: D*[1-exp(-beta(r-r0)]**2. The columns are:

#pdb index for atom i, pdb index for atom j, bond type (3 for Morse), r0 (RS), D (RS), beta (RS), r0 (PS), D (PS) beta (PS)

NOTE: for any other bond type, give the parameters as in GROMACS topology.

[bcon] directive contains constraints between pairs of atoms. The constraints are gives as bonds of type 6 or 10 which does not generate exclusions. The format is the same as in GROMACS topology.

NOTE: If you want to change any of the angles, torsions and impropers for EVB atoms (passed through the .opls files), you cand do that under the [angles], [torsions] or [impropers] directives following the same format as in GROMACS topology.

[soft-pairs] directive contain the soft repulsion potential defined for pairs of atoms. Any pair given here will substitute the pair built from data found under [soft-core] directive. The columns are:

#pdb index for atom i, pdb index for atom j, 9, beta (RS), A (RS), beta (PS), A (PS)

NOTE: Soft repulsion potentials are passed to GROMACS as tabulated bonds of type 9 (so the 3rd column is always '9').

NOTE: RS means Reactants State and PS means Products State (or states A and B as they are usually reffered to in GROMACS manual).