Input files (input structures, topology, Gromacs and Plumed input files, analysis scripts) for simulations used to demonstrate functionality of combined thermodynamic integration and flying Gaussian method. The method is demonstrated on N-acetylproline. pKa for this weak acid is known for cis and trans conformers. The aim of this work is to predict pKa for equilibrium. Thermodynamic integration is used to calculate Alchemistically the value of pKa. Flying Gaussian method is used to accelerate cis/trans isomerization. Reweighting with an innovative thermodynamic cycle redefinition is used. Tested on OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Submission scripts are provided. Files: fg/AceProO/frame0.gro to frame49.gro Initial structures for flying Gaussian simulation of cis/trans equilibrium of AcePro[O-]. fg/AceProO/mtd.mdp Gromacs parameters for flying Gaussian simulation of cis/trans equilibrium of AcePro[O-]. fg/AceProO/plumed.dat Plumed parameters for flying Gaussian simulation of cis/trans equilibrium of AcePro[O-]. fg/AceProO/runit.sh Script for flying Gaussian simulation of cis/trans equilibrium of AcePro[O-]. fg/AceProO/topol.top Gromacs topology for flying Gaussian simulation of cis/trans equilibrium of AcePro[O-]. fg/AceProOH/acepro.top Gromacs topology for flying Gaussian simulation of cis/trans equilibrium of AcePro[OH]. fg/AceProOH/frame0.gro to frame49.gro Initial structures for flying Gaussian simulation of cis/trans equilibrium of AcePro[OH]. fg/AceProOH/mtd.mdp Gromacs parameters for flying Gaussian simulation of cis/trans equilibrium of AcePro[OH]. fg/AceProOH/plumed.dat Plumed parameters for flying Gaussian simulation of cis/trans equilibrium of AcePro[OH]. fg/AceProOH/runit.sh Script for flying Gaussian simulation of cis/trans equilibrium of AcePro[OH]. fg/analysis/otfr.py Preprocessing script for analysis of flying Gaussian simulation of cis/trans equilibria. fg/analysis/TI2.c Calculator of errors. Can be compiled by 'gcc -o TI2.out TI2.c -lm'. ti/cis/acepro.top Gromacs topology for thermodynamic integration simulation of cis-AcePro. ti/cis/frame0.gro Initial structure for thermodynamic integration simulation of cis-AcePro. ti/cis/em_steep.mdp Minimization parameters for thermodynamic integration simulation of cis-AcePro. ti/cis/npt.mdp NPT simulation parameters for thermodynamic integration simulation of cis-AcePro. ti/cis/nvt.mdp NVT simulation parameters for thermodynamic integration simulation of cis-AcePro. ti/cis/md.mdp Production simulation parameters for thermodynamic integration simulation of cis-AcePro. ti/cis/prepare_system.py Script to prepare a series of thermodynamic integration simulations of cis-AcePro. ti/cis/runit.sh Script for thermodynamic integration simulation of cis-AcePro. ti/trans/acepro.top Gromacs topology for thermodynamic integration simulation of trans-AcePro. ti/trans/after_mtd1_3.gro Initial structure for thermodynamic integration simulation of trans-AcePro. ti/trans/em_steep.mdp Minimization parameters for thermodynamic integration simulation of trans-AcePro. ti/trans/npt.mdp NPT simulation parameters for thermodynamic integration simulation of trans-AcePro. ti/trans/nvt.mdp NVT simulation parameters for thermodynamic integration simulation of trans-AcePro. ti/trans/md.mdp Production simulation parameters for thermodynamic integration simulation of trans-AcePro. ti/trans/prepare_system.py Script to prepare a series of thermodynamic integration simulations of trans-AcePro. ti/trans/runit.sh Script for thermodynamic integration simulation of trans-AcePro. ti/analysis/cropit.sh Preprocessing script for analysis of thermodynamic integration simulations. ti/analysis/TI2.c Calculator of errors. Can be compiled by 'gcc -o TI2.out TI2.c -lm'. tifg/run1/acepro.top Gromacs topology for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/frame0.gro Initial structure for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/em_steep.mdp Minimization parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/npt.mdp NPT simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/nvt.mdp NVT simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/md.mdp Equilibration parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/mtd.mdp Production simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/plumed.dat Plumed parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/prepare_system.py Preparation script for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run1/hostfile Hostfile for combined flying Gaussian and thermodynamic integration simulation of AcePro (to be used if the number of physical core is less than 48, run 1). tifg/run1/runit.sh Script for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 1). tifg/run2/acepro.top Gromacs topology for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/frame0.gro Initial structure for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/em_steep.mdp Minimization parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/npt.mdp NPT simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/nvt.mdp NVT simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/md.mdp Equilibration parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/mtd.mdp Production simulation parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/plumed.dat Plumed parameters for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/prepare_system.py Preparation script for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/run2/hostfile Hostfile for combined flying Gaussian and thermodynamic integration simulation of AcePro (to be used if the number of physical core is less than 48, run 2). tifg/run2/runit.sh Script for combined flying Gaussian and thermodynamic integration simulation of AcePro (run 2). tifg/analysis/otfr.py Preprocessing script for analysis of combined flying Gaussian and thermodynamic integration simulations. tifg/analysis/TI2.c Calculator of errors. Can be compiled by 'gcc -o TI2.out TI2.c -lm'.