Input files (input structures, topology, Plumed input files) for simulations used to demonstrate functionality of Flying Gaussian algorithm (J. Chem. Theory Comput. 2016, 12, 4644-4650). The method simulates a molecular system in multiple replicas and enhances sampling by disfavoring states that are close to each other in different replicas. Input files for Flying Gaussian simulation of alanine dipeptide in vacuum and water, cis/trans isomerization of Ace-(Pro)n-NH2 and Met-enkephalin are provided. In most cases, longer simulation have to be done to reproduce results from the article. Scripts for calculation of free energy surfaces by reweighing are provided. Input data for cis/trans isomerization of Ace-(Pro)n-NH2 were modified relative to the publication in the way that implicit solvent was replaced by explicit one due to lack of support for implicit solvents in recent Gromacs versions. Tested on OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Submission scripts are provided. Directories: acealanmevacuum - demonstration of Flying Gaussian method on alanine dipeptide in vacuum with Ramachandran torsions as CVs acealanmewater8 - demonstration of Flying Gaussian method on alanine dipeptide in water with Ramachandran torsions as CVs and 8 walkers acealanmewater16 - demonstration of Flying Gaussian method on alanine dipeptide in water with Ramachandran torsions as CVs and 16 walkers acealanmewater32 - demonstration of Flying Gaussian method on alanine dipeptide in water with Ramachandran torsions as CVs and 32 walkers acealanmewater64 - demonstration of Flying Gaussian method on alanine dipeptide in water with Ramachandran torsions as CVs and 64 walkers AceProNH2 - demonstration of Flying Gaussian method on AceProNH2 in water with cis/trans isomerization CV and 20 walkers AceProProNH2 - demonstration of Flying Gaussian method on AceProProNH2 in water with cis/trans isomerization CV and 40 walkers AceProProProNH2 - demonstration of Flying Gaussian method on AceProProProNH2 in water with cis/trans isomerization CV and 64 walkers metenkephalin - demonstration of Flying Gaussian method on Met-enkephalin in water with CVs taken from J. Chem. Theory Comput. 2010, 612, 3640-3646 and 20 walkers Files: *.gro - input structures after minimization or equilibration *.mdp - Gromacs simulation command files *.top – Gromacs topology files hostfile - file used by MPI justcommands.sh - commands to be run otfr.py - reweighing Python scripts plumed.dat - plumed input files runit.sh - actual scripts used in the simulations