Input files (input structure, topology, Plumed input) for simulations used to demonstrate
functionality of anncolvar (https://github.com/spiwokv/anncolvar). Input files for metadynamics
simulation of cyclooctane derivative in vacuum with three Isomap CVs, metadynamics (mtd),
parallel tempering (ptmd) and parallel tempering metadynamics (ptmtd) of Trp-cage in water with
solvent-accessible surface area and alpha-RMSD CVs are provided. Tested on OpenMPI4.0.0,
Gromacs 2018.5 and Plumed2.5.0. Scripts provided.

Input files:
anncolvar/c8/after_em.gro - Gromacs input structure of cyclooctane derivative in vacuum

anncolvar/c8/justcommands.sh - script to run the simulations (can be updated to specify
software location)

anncolvar/c8/molecule_gmx.top - Gromacs General Amber Force Field topology of cyclooctane
derivative in vacuum

anncolvar/c8/mtd.mdp - Gromacs instruction file (10 ns, 300 K). In order to replicate the data
in the article it is necessary to prolong the simulation

anncolvar/c8/plumed.dat - Plumed input file

anncolvar/c8/reference2.pdb - Plumed reference PDB file used as a template for RMS fitting

anncolvar/c8/runit.sh - actual script used to run the simulation

anncolvar/trpcage/mtd/justcommands.sh - script to run the simulations (can be updated
to specify software location)

anncolvar/trpcage/mtd/md.mdp - Gromacs instruction file (0.5 ns, 300 K), in order to replicate
the data in the article it is necessary to prolong the simulation

anncolvar/trpcage/mtd/newreference.pdb - Plumed reference PDB file used as a template for
RMS fitting

anncolvar/trpcage/mtd/npt.cpt - Gromacs input checkpoint of Trp-cage in water

anncolvar/trpcage/mtd/npt.gro - Gromacs input structure of Trp-cage in water

anncolvar/trpcage/mtd/plumed.dat - Plumed input file

anncolvar/trpcage/mtd/reference.pdb - Plumed reference PDB file used as a template for MOLINFO

anncolvar/trpcage/mtd/runit.sh - actual script used to run the simulation

anncolvar/trpcage/mtd/topol.top - Gromacs Amber99SB-ILDN topology of Trp-cage in water

anncolvar/trpcage/ptmd/hostfile - file used by runit.sh to run MPI with higher number of
processes than the number of physical cores

anncolvar/trpcage/ptmd/justcommands.sh - script to run the simulations (can be updated
to specify software location)

anncolvar/trpcage/ptmd/md_0.mdp - md_31.mdp - Gromacs instruction file (1 ns, 300 K),
in order to replicate the data in the article it is necessary to prolong the simulation

anncolvar/trpcage/ptmd/mtd0_0.cpt - mtd0_31.cpt - Gromacs input checkpoints of Trp-cage
in water

anncolvar/trpcage/ptmd/mtd0_0.gro - mtd0_31.gro - Gromacs input structure of Trp-cage
in water

anncolvar/trpcage/ptmd/newreference.pdb - Plumed reference PDB file used as a template
for RMS fitting

anncolvar/trpcage/ptmd/plumed.dat - Plumed input file

anncolvar/trpcage/ptmd/reference.pdb - Plumed reference PDB file used as a template for
MOLINFO

anncolvar/trpcage/ptmd/runit.sh - actual script used to run the simulation

anncolvar/trpcage/ptmd/topol.top - Gromacs Amber99SB-ILDN topology of Trp-cage in water

anncolvar/trpcage/ptmtd/demuxit.py - Demuxing script

anncolvar/trpcage/ptmtd/diditfold.py - Scirpt to detect folding in demuxed collective
variable files

anncolvar/trpcage/ptmtd/hostfile - file used by runit.sh to run MPI with higher number
of processes than the number of physical cores

anncolvar/trpcage/ptmtd/justcommands.sh - script to run the simulations (can be updated
to specify software location)

anncolvar/trpcage/ptmtd/md_0.mdp - md_31.mdp - Gromacs instruction file (1 ns, 300 K),
in order to replicate the data in the article it is necessary to prolong the simulation

anncolvar/trpcage/ptmtd/mtd0_0.cpt - mtd0_31.cpt - Gromacs input checkpoints of Trp-cage
in water

anncolvar/trpcage/ptmtd/mtd0_0.gro - mtd0_31.gro - Gromacs input structure of Trp-cage
in water

anncolvar/trpcage/ptmtd/newreference.pdb - Plumed reference PDB file used as a template
for RMS fitting

anncolvar/trpcage/ptmtd/plumed.dat - Plumed input file

anncolvar/trpcage/ptmtd/reference.pdb - Plumed reference PDB file used as a template for
MOLINFO

anncolvar/trpcage/ptmtd/runit.sh - actual script used to run the simulation

anncolvar/trpcage/ptmtd/topol.top - Gromacs Amber99SB-ILDN topology of Trp-cage in water