Input files (input structures, topology, Plumed input) for simulations used to demonstrate
functionality of Close Structure algorithm (J. Chem. Phys. 2017, 146, 115101). The method
replaces frequent calculations of root mean square deviations in Path collective variables
or Property Map collective variables. This accelerates simulations. Input files for
metadynamics simulation of cyclooctane derivative in vacuum and Trp-cage in implicit solvent
with two or three, respectively, Isomap CVs (with and without Close Structure). Tested on
OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Scripts provided.

Directories:
cyclo/close - metadynamics simulation of cyclooctane derivative in vacuum with three Isomap
CVs with Close Structure

cyclo/normal - metadynamics simulation of cyclooctane derivative in vacuum with three Isomap
CVs without Close Structure

trpcage/close - metadynamics simulation of Trp-cage in implicit solvent with two Isomap CVs
with Close Structure

trpcage/normal - metadynamics simulation of cTrp-cage in implicit solvent with two Isomap
CVs without Close Structure

Files:
after_em.gro - cyclooctane input structure after minimization

after_em1.gro - Trp-cage input structure after minimization

COLVAR - collective variable record

HILLS - hills record

ions.itp - ion topology

justcommands.sh - commands to be run

md1.mdp - Gromacs simulation command file for Trp-cage, longer simulations are needed to
reproduce the results of the article

molecule_gmx.top - cyclooctane topology

mtd.mdp - Gromacs simulation command file for cyclooctane, longer simulations are needed
to reproduce the results of the article

plumed.dat - plumed input file for Trp-cage

plumed_v2.dat - plumed input file for cyclooctane

reference.pdb - reference coordinates with input file for cyclooctane

reframe.pdb - reference coordinates with input file for Trp-cage

runit.sh - actual script used in the simulation

trpcage.top - Trp-cage topology