Fork me on GitHub

OpenMM Molecular Dynamics

Run NVE, NVT or stochastic dynamics using OpenMM.


Usage: ffxc DynamicsOpenMM [-ho] [--cf=0.01] [-b=Bussi] [-d=1.0] [-F=XYZ] [-i=Verlet] [-k=1.0] [-n=1000000] [-p=0] [-q=91.0] [-r=0.25] [-t=298.15] [-w=10.0] [-z=100] files...
Run dynamics on a system using OpenMM.
    files...                XYZ or PDB input files.
    --cf, --friction=0.01   Coefficient of friction to be used with the Langevin integrators.
-b, --thermostat=Bussi      Thermostat: [Adiabatic / Berendsen / Bussi].
-d, --dt=1.0                Time discretization step in femtoseconds.
-F, --fileFormat=XYZ        Choose file type to write [PDB/XYZ].
-h, --help                  Print this help message.
-i, --integrator=Verlet     Integrator: [Beeman / Respa / Stochastic / Verlet].
-k, --checkpoint=1.0        Interval to write out restart files (.dyn, .his, etc).
-n, --numberOfSteps=1000000 Number of molecular dynamics steps.
-o, --optimize              Optimize and save low-energy snapshots.
-p, --npt=0                 Specify use of a MC Barostat at the given pressure; the default 0 disables NPT (atm).
-q, --collision=91.0        Collision frequency for the Anderson thermostat.
-r, --report=0.25           Interval to report thermodynamics (psec).
-t, --temperature=298.15    Temperature (Kelvin).
-w, --write=10.0            Interval to write out coordinates (psec).
-z, --trajSteps=100         Number of steps for each OpenMM MD cycle.