Classical MD with NAMD

Classical MD can be performed with NAMD via an MD object, as used in the Solvation workflow. The following options are for generic MD settings. For NAMD specific options see NAMD.

General options

boundary

Periodic boundary conditions (PBCs). Allowed values are:

'periodic' (default): With PBCs
'sphere', 'spherical', or 'droplet': Non-periodic without PBCs

chk: (default: '') Check filename to write out

dcd: (default: '') DCD filename to write out

driver: (default: 'dl_poly') We currently only support driver='namd' for classical MD simulations on biomolecular systems

ensemble: (default: 'NPT') Ensemble of simulation. No ensemble is applied periodic is 'sphere', 'spherical', or 'droplet'

ff: (default: 'charmm') Name of forcefield scheme. We currently only support the CHARMM-type forcefield (not to be confused with the CHARMM program). See INSTALL for installing the CHARMM forcefield data

fix: (default: []) List of indices of atoms to fix during an MD simulation. In practice, such a list is typically obtained by Fragment.select()

freq_chk: (default: -1) Frequency of writing out checkpoint files. If undefined the number will be determined by ChemShell as ceil(nsteps/100) when nsteps is greater than 100 or 1 otherwise

freq_dcd: (default: -1) Frequency of writing out DCD files. If undefined the number will be determined by ChemShell as ceil(nsteps/100) when nsteps is greater than 100 or 1 otherwise

freq_xst: (default: -1) Frequency of writing out XST files. If undefined the number will be determined by ChemShell as ceil(nsteps/100) when nsteps is greater than 100 or 1 otherwise

freq_out_energy: (default: -1) Frequency of writing out energies. If undefined the number will be determined by ChemShell as ceil(nsteps/100) when nsteps is greater than 100 or 1 otherwise

freq_out_pressure: (default: -1) Frequency of writing out pressures. If undefined the number will be determined by ChemShell as ceil(nsteps/100) when nsteps is greater than 100 or 1 otherwise

langevin: (default: True) Perform Langevin dynamics

langevin_temperature: (default: None) Temperature of Langevin dynamics

langevin_damping: (default: 1 ps^-1) Damping coefficient for Langevin dynamics

langevin_H: (default: False) Apply Langevin dynamics to hydrogen atoms

langevin_piston: (default: False) Use the Langevin piston pressure control method

langevin_piston_target: (default: 1.01325 bar) Target pressure of the Langevin piston method

langevin_piston_period: (default: 100.0 femtoseconds) Barostat oscillation time scale for the Langevin piston

langevin_piston_decay: (default: 50.0 femtoseconds) Barostat damping time scale for the Langevin piston

langevin_piston_temp: (default: 293.15 Kelvin) Barostat noise temperature for the Langevin piston

minimise: (default: 100) Number of energy minimisation steps to take, typically before an MD simulations starts

nsnapshots: (default: 10) Number of snapshots to take after a simulation is successfully run. They will be taken only from the second half out of a trajectory to use equilibrated data as much as possible. There is also an independent tool for taking snapshots from an existing DCD trajectory: tools.takeSnapshots()

nsteps: (default: 100) Number of MD steps to simulate

pbc_wrap: (default: []) List of atom indices to perform PBC wrapping

rigid

Use the rigid bond model by making hydrogen—connected–atom constrained. Accepted values are:

'all' (default) Constrain all hydrogen—connected–atom bonds to the positions defined by the forcefield parameters. Also Constrain all hydrogen—oxygen—hydrogen angles in water molecules
'water' Constrain only hydrogen—oxygen bonds and hydrogen—oxygen—hydrogen angles of water molecules to the positions defined by the forcefield parameters
'none' No rigid bond constraint

seed: (default: 2020) Seed number for generating random numbers

spheric_r0: (default: -1.0 Bohr) Spherical radius r_SBC in Bohr for non-periodic simulations with spherical boundary conditions (SBCs). The default value -1.0 means that ChemShell will determine it by calculating the system’s stretching radius. When defined, it must be a positive decimal number.

spheric_k: (default: 10.0) Force constant k_SBC for the SBCs harmonic potential. The potential is calculated as P_SBC = k_SBC(||r_i - r_centre|| - r_SBC)**exp_SBC

spheric_exponent: (default: 2) Exponent exp_SBC for the SBCs harmonic potential. A typical value is 2 or 4

temperature: (default: 293.15 Kelvin) Temperature of simulation

theory: (default: None) Theory <theory> object for evaluating the energies and gradients

timestep: (default: 1.0 femtosecond) Timestep of MD simulation