Force fields
To setup a simulation using hybrid structures and topologies the modified force field files are required. After downloading and extracting the force fields set the GMXLIB variable to the "mutff45" directory.
Amino acid mutations: mutff45.tar.gz
Nucleic acid (DNA) mutations: mutff45dna.tar.gz

For a large scale protein mutation scan running pmx from the command-line might be more convenient. pmx can be downloaded from the git repository:

Pre-generated hybrid structure and topology files for the capped GXG tripeptides that can be used as an approximation for the unfolded state of a protein when calculating protein thermodynamic stabilities:

.mdp files
Simulation with these .mdp files use cutoff scheme "Group" which has been replaced by a "Verlet" scheme in the Gromacs 5.x versions. However, so far we have mostly tested the free energy estimates with the earlier Gromacs version 4.6. Download the mdp files.

Description of the files
em_A.mdp: energy minimization in state A (lambda=0)
em_B.mdp: energy minimization in state B (lambda=1)
equilibration_A.mdp: equilibrium simulations in state A (lambda=0)
equilibration_B.mdp: equilibrium simulations in state B (lambda=1)
transition_A2B.mdp: fast transition from A to B (lambda goes from 0 to 1)
transition_B2A.mdp: fast transition from B to A (lambda goes from 1 to 0)

Gromacs 4.6 with an alternative soft-core function
Using the default Gromacs soft-core may cause artifacts during the non-equilibrium transitions. We have implemented an alternative soft-core version into Gromacs 4.6.2 version (unfortunately GPU support here is not yet supported with the free energy calculations): gromacs462_newsc.tar The default soft-core parameters in this Gromacs version are hardcoded following the original publication: DOI: 10.1021/ct300220p