README.md

Input File Reference

SPONGE automatically reads mdin.spg.toml from the working directory. If it is absent, the legacy mdin.txt input is also recognized. Use -mdin to select another input file explicitly:

SPONGE -mdin mdin.spg.toml

Table of Contents

• Core Parameters — mode, steps, time step, cutoff
• Input/Output — file specification and output control
• Thermostat — thermostat algorithms and parameters
• Barostat — barostat algorithms and parameters
• Restrain — atom-coordinate restrain input
• Constraints — SETTLE / SHAKE
• Neighbor List — neighbor list configuration
• PME Electrostatics — Particle Mesh Ewald
• Collective Variables — CV definitions and examples
• Enhanced Sampling — CV, MetaD, SITS
• SinkMeta — detailed meta / SinkMeta parameter reference
• Advanced — device, wall constraints, ReaxFF, plugins

Quick Examples

NVT

md_name = "NVT water"
mode = "nvt"
step_limit = 50000
dt = 0.002
cutoff = 8.0
default_in_file_prefix = "WAT"
constrain_mode = "SHAKE"
target_temperature = 300.0
write_information_interval = 1000

[thermostat]
mode = "middle_langevin"
tau = 0.1
seed = 2026

NPT

md_name = "NPT water"
mode = "npt"
step_limit = 100000
dt = 0.002
cutoff = 8.0
default_in_file_prefix = "WAT"
constrain_mode = "SHAKE"
target_temperature = 300.0
target_pressure = 1.0
write_information_interval = 1000

[thermostat]
mode = "middle_langevin"
tau = 0.1
seed = 2026

[barostat]
mode = "andersen_barostat"
tau = 0.1
update_interval = 10

Energy Minimization

md_name = "minimization"
mode = "minimization"
step_limit = 1000
default_in_file_prefix = "system"
cutoff = 8.0
write_information_interval = 100