| bomlev | undef | set bomb level |
| prnlev | undef | set print level |
| |
| param | 36 | parameter set: 19 (CHARMM19), 22 (CHARMM22), opls, a94 (amber 94), eef1, mmff |
| xpar | undef | extra parameter files |
| |
| |
| cmap | 1 | use CMAP correction |
| geomvdw | undef | geometric combination of sigmas for OPLS L-J terms |
| scale14 | 1.0 | 1-4 scaling |
| |
| epsilon | 1.0 | dielectric constant for non-bonded interactions |
| cutnb | undef | cutoff for non-bonded list generation |
| cutoff | undef | cutoff for non-bonded interactions |
| cuton | undef | onset of switching function for non-bonded interaction |
| cut | 1 | use cutoff |
| trunc | undef | shift/fshift/switch/fswitch |
| |
| shake | 0 | use shake |
| shaketol | 1.0E-8 | shake tolerance |
| |
| periodic | 1 | use periodic boundaries |
| ewald | 1 | use Ewald for explicit solvent |
| npme | undef | 64, # number of grid points for PME grid |
| npmex | undef | number of grid points in x direction |
| npmey | undef | number of grid points in y direction |
| npmez | undef | number of grid points in z direction |
| pmegrid | undef | pme grid spacing |
| margin | undef | patch margin |
| ldb | 1 | load balancing |
| |
| boxshape | undef | box shape for periodic boundaries |
| boxsize | undef | box size |
| boxx | undef | box x dimension |
| boxy | undef | box y dimension |
| boxz | undef | box z dimension |
| |
| dynens | 'NVT' | dynamics ensemble 'NVT', 'NPT', 'NPH', 'NVE' |
| dynber | 0 | use Berendsen thermostat |
| tcouplefile | undef | file with Berendsen time constant |
| dyntstep | 0.002 | dynamics time step in picoseconds |
| dynsteps | 100 | dynamics steps |
| dyntemp | 298 | dynamics temperature |
| dynseed | undef | dynamics random seed |
| dyntrfrq | undef | trans/rot removal frequency |
| dynremovecom | undef | remove center of mass motion when restarting |
| dyneqfrq | 0 | velocity reassignment frequency |
| dynscalefrq | 0 | temperature rescaling frequency |
| dynoutfrq | 500 | frequency of energy/trajectory output |
| dynouttime | 1000 | frequency of writing timing information |
| dynrestfrq | 1000 | frequency of saving restart files |
| dyneoutfrq | undef | frequency of writing out energy information |
| dynupdnb | 10 | update of non-bonded list |
| dynpress | 1.00 | the pressure (in atm) for NPT simulations |
| dynpperiod | 200.0 | gamma value for NPT simulations |
| dynpdecay | 100.0 | Langevin piston mass for NPT simulations |
| dynnpat | 0 | constant surface area for membrane simulations |
| |
| lang | 1 | flag for running Langevin dynamics |
| langBAOAB | 0 | BAOAB integrator from Leimkuhler et al. |
| langfbeta | 1.0 | friction coefficient for Langevin dynamics |
| |
| tmdrmsd | undef | set initial TMD RMSD to turn it on |
| tmdrmsdto | undef | set final TMD RMSD, by default equal to initial RMSD |
| tmdk | 100 | force constant |
| tmdoutfrq | undef | TMD output frequency |
| tmdref | undef | TMD reference file |
| |
| tmdrmsd2 | undef | set initial TMD RMSD to turn it on |
| tmdrmsd2to | undef | set final TMD RMSD, by default equal to initial RMSD |
| tmdk2 | 100 | force constant |
| tmdref2 | undef | TMD reference file |
| |
| mmtsbserver | undef | MMSTB server host name |
| mmtsbport | undef | MMTSB server port number |
| mmtsbsid | undef | MMTSB server ID |
| mmtsbjobid | undef | MMTSB job ID |
| mmtsbcycle | undef | replica exchange cycle length |
| |
| cons | 0 | set to 1 and provide reference file through -consref |
| |
| colvars | undef | turn on and provide config file for colvars |
| |
| extrabonds | undef | turn on and provide extra bonds input file |
| |
| minsteps | undef | minimize |
| |
| |
| |
| |
| |
