Sample Input File

Let’s run the command “./spdyn -h ctrl md > INP“. You will obtain a new file named INP.

$ /home/user/genesis/bin/spdyn -h ctrl md > INP
$ more INP
topfile =   # topology file
parfile = sample.par   # parameter file
psffile = sample.psf   # protein structure file
pdbfile = sample.pdb   # PDB file
electrostatic = PME    # [CUTOFF,PME]
switchdist    = 10.0   # switch distance
cutoffdist    = 12.0   # cutoff distance
pairlistdist  = 13.5   # pair-list distance
integrator    = LEAP   # [LEAP,VVER]
nsteps        = 100    # number of MD steps
timestep      = 0.001  # timestep (ps)
eneout_period = 10     # energy output period
rigid_bond    = NO     # constraints all bonds involving hydrogen
ensemble      = NVE    # [NVE,NVT,NPT]
tpcontrol     = NO     # thermostat and barostat
type          = PBC    # [PBC]

Here, we used “INP” for the file name, but of course you can choose the name as you like. This control file contains minimal information about MD parameters, and other “hidden” parameters are set to default. (To see non-standard option, please use ctrl_all instead of ctrl; see example below.) This control file will perform a 100 step MD simulation with the time step of 1 fs in the NVE ensemble under the periodic boundary condition (PBC), where the CHARMM force filed and the Particle Mesh Ewald method are used. To use the CHARMM force field, we need to prepare topfileparfilepdbfile, and psffile of the [INPUT] section. Topology file (topfile) and parameter file (parfile) are available from the MacKerell’s homepage. For psffile and pdbfile, psfgen, VMD, or CHARMM might be used. You must edit this template control file according to your simulation system. If you wanna know other keywords or parameters, such for temperature and pressure regulation in the NPT simulation, please read the user manual or run the following command:

$ /home/user/genesis/bin/spdyn -h ctrl_all md > INP

This will generates all available keywords and parameters.