REMD

REMD is a replica exchange molecular dynamics simulation package for water especially confined in nanopore (e.g. nanotube and nano slit). Please refer to https://doi.org/10.1073/pnas.1701609114 for use case. If you use this package, please cite out paper above.

requirement

• g++ 5.0 or later

(optional)

• Intel oneAPI 2021.3 or later
• NVIDIA CUDA 8.0 or later

input parameter

• input_prefix: prefix for input files (e.g. /home/user/work/input/)
• output_prefix: prefix for output files (e.g. /home/user/work/output/)
• gro_in: prefix of input gro file (e.g. gro_file). Input gro file path is ${input_prefix}${gro_in}XXXX.gro (XXXX is replica number in 4 digit).
• gro_out: prefix of output gro file (e.g. gro_file). Output gro file path is ${output_prefix}${gro_out}XXXX.gro (XXXX is replica number in 4 digit).
• trr_in: prefix of input trr file (e.g. trr_file)
• trr_out: prefix of output trr file (e.g. trr_file)
• chk_in: prefix of input check point file (e.g. chk_file). Input checkpoint file path is ${input_prefix}${chk_in}XXXX.chk (XXXX is replica number in 4 digit).
• chk_out: prefix of output check point file (e.g. chk_file). Output checkpoint file path is ${output_prefix}${chk_out}XXXX.chk (XXXX is replica number in 4 digit).
• cdv_out: prefix of output cdview file. Output checkpoint file path is ${output_prefix}${chk_out}XXXX_sYYYYYYY.cdv (XXXX and YYYYYYY are replica number and interval number).
• nmol: number of molecules
• natom: number of atoms
• nsite: number of site of water model.
• dt: time step (fs)
• rcut: cutoff length (angstrom)
• rswitch: length where switching function starts (angstrom)
• tconstant: choise of thermostat. 0 for not controlling temperature. 1 for Nose-Poincare thermostat. 2 for velocity scaling.
• temp_max: maximum temperature (K)
• temp_min: minimum temperature (K)
• tstat_mass: mass for thermostat
• pconstant: choise of barostat. 0 for not controlling pressure. 1 for 3D Andersen barostat. 2 for 1D Andersen barostat which controls pressure of z-direction. 3for 2D Andersen barostat which controls pressure of xy-direction.
• press_max: maximum pressure (Pa)
• press_min: minimum pressure (Pa)
• bstat_mass: mass for barostat
• ninterval: number of intervals (total number of steps is ${ninterval}*${interval}).
• interval: number of steps between replica exchange attempt.
• energy_interval: number of intervals between output energy
• snap_interval: number of intervals between output cdvidew snapshot
• chk_interval: number of intervals between output check point file
• rem_type: type of replica exchange. 0 for no replica exchange. 1 for origilan replcia exchange method.
• nreplica: number of replicas. ${nreplica} must be ${ntemp}*${npress}.
• ntemp: number of temperature.
• npress: number of pressure.
• energy_max: maximum energy for energy histogram (kJ / mol)
• energy_min: minimum energy for energy histogram (kJ / mol)
• volume_max: maximum volume for volume histogram (angstrom^3 / mol)
• volume_min: minimum volume for volume histogram (angstrom^3 / mol)
• gen_vel: generate random velocity (1) or not (0)
• cond_mode: generate temperature conditions as geometric series (0), or optimized with previous heat capacity data (1) which require phys_value.dat in input directory.
• init_scaling: apply velocity scaling before simulation start (1) or not (0). 1 is recommended.
• ngpus: number of GPUs to use.
• gpu_offset: offset for gpu number. if gpu_offset=2 and ngpu=2, GPU 2 and 3 is used.
• confined: dimension of confined system. (0, 1 or 2)
• nfwall: number of points for linear interpolation of wall force/energy.
• wall_length: radius of carbon nanotube when confined=1 and slit width of nano slit when confined=2 (angstrom).
• sgm_wall: sigma of LJ potential of nanopore atom. (e.g. 3.277 for carbon atom).
• eps_wall: epsilon of LJ potential of nanopore atom. (e.g. 0.3886 for carbon atom).
• rho_wall: surface density of nanopore atoms. (e.g. 0.38016 for carbon nanotube)

how to run

REMD_ROOT is the directory of this repository.

cd ${REMD_ROOT}

make -f makefile.xxx # xxx is gnu, intel or cuda

cd ${WORKING_DIRECTORY}

mkdir -p ${OUTPUT_DIRECTORY_PATH}/cdv

${REMD_ROOT}/src/md.out ${INPUT_DIRECTORY_PATH}/XXX.inp