Molecular Dynamics

Running a plain MD simulation with the internal dynamics module.

Table of contents

1. The --dynamics runtype
2. Simulation settings
3. Thermostats
4. Where MD is used internally

The --dynamics runtype

--dynamics (alias --dyn) runs a straightforward molecular dynamics simulation with the internal MD module, a velocity Verlet integrator driving the same calculators as every other runtype. It is the same engine that the metadynamics of the conformational search is built on, here without any bias potential.

The settings live in a [dynamics] block of a TOML input file:

crest input.toml

# Molecular dynamics simulation
input   = "struc.xyz"
runtype = "dynamics"
threads = 4

[calculation]
[[calculation.level]]
method = "gfn2"

[dynamics]
length = 2.0        # simulation length in ps
tstep  = 2.0        # time step in fs
dump   = 100.0      # write a snapshot every 100 fs
temp   = 300.0      # target temperature in K
shake  = 2          # constrain bonds (2 = all bonds)

   ─────────────── Molecular Dynamics Settings ──────────────
  Simulation type       :       NVT
  MD time (length)      :      2.00 ps
  dt (timetep)          :      2.00 fs
  temperature           :    300.00 K
  max steps             :      1000
  block length (av.)    :      2500
  dumpstep(trj) /fs     :    100.00 (50)
  # deg. of freedom     :        25
  thermostat            : Berendsen
  SHAKE constraint      :      true
  # SHAKE bonds         :        11 (all bonds)
  hydrogen mass /u      :   2.00000
 ──────────────────────────────────────────────────────────

                            [ ... ]

 average properties
 ------------------------------------------
 <Epot>                  -14.53223496 Eh
 <Ekin>                    0.01111890 Eh
 <Etot>                  -14.52111606 Eh
 <T>                           280.89 K
 Tvar                         5362.51 K²
 σ(T)                           73.23 K
 ------------------------------------------

 normal MD termination
 MD run completed successfully
 Trajectory written to crest_dynamics.trj.xyz

The settings block echoes what the simulation will actually do, which is worth reading before a long run: the 2 ps length at a 2 fs time step gives 1000 steps, and the 100 fs dump interval means every 50th step is written. Setting a target temperature implies a thermostat, so the simulation type is reported as NVT.

At the end, block averages of the potential, kinetic and total energy are printed together with the mean temperature and its fluctuation. The trajectory is written to crest_dynamics.trj.xyz, and a crest_0.mdrestart file holds the final state.

Simulation settings

The keys of the [dynamics] block:

SHAKE removes the fastest vibrations from the integration, which is what allows a 2 fs step to be used at all. With shake = 2 the printout confirms how many bonds were constrained. Increasing hmass (hydrogen mass repartitioning) permits even larger steps.

Thermostats

CREST 3.1

CREST 3.1 adds two stochastic thermostats alongside the existing Berendsen one, selected with the thermostat key:

For example, to run the same simulation in the correct canonical ensemble:

[dynamics]
length     = 2.0
tstep      = 2.0
dump       = 100.0
temp       = 300.0
thermostat = "bussi"    # stochastic velocity rescaling (BDP/CSVR)

The chosen algorithm is reported in the settings block, and thermostat = "off" switches the header from NVT to NVE:

  Simulation type       :       NVT
  thermostat            : Bussi-Donadio-Parrinello

Where MD is used internally

The conformational search workflows do not call this runtype, but they use the same module. The iMTD-GC algorithm runs metadynamics, the same integrator with an additional history-dependent bias pushing the system away from structures it has already visited, and regular MD is used for the subsequent sampling steps. Settings such as tstep, shake and hmass carry over to those workflows.