| param | "ff94" | force field: ff94, ff96, ff86, ff98, ff99, ff02, ff02EP, gaff |
| sdsteps | 50 | number of minimization steps for steepest descent min. |
| minsteps | 300 | number of minimization steps for ABNR min. |
| minetol | 1E-2 | energy gradient tolerance for min. |
| minstepsz | 0.005 | initial min. step size |
| minoutfrq | 10 | minimization output frequency |
| gb | undef | use GB potential: tc6, tc, obc, jsb, mgb |
| gbsa | 0 | include surface area term in GB potential |
| gbeps | 80 | external dielectric for GB |
| cutoff | 14 | cutoff for non-bonded interactions |
| cut | 1 | use cutoff |
| epsilon | 1.0 | dielectric constant |
| dielec | 'CDIE' | dielectric: cdie, rdie |
| dynsteps | 100 | dynamics steps |
| dyntstep | 0.002 | dynamics step size |
| dyntemp | 300 | dynamics temperature |
| dynitemp | undef | dynamics initial temperature |
| dynseed | undef | random number generator seed |
| dynoutfrq | 10 | minimization output frequency |
| restrain | 0 | restraints from restraint file |
| rex | 0 | flag for running replica exchange |
| lambda | undef | lambda value for thermodynamic integration |
| saltcon | undef | salt concentration for use with GB |
| rexmode | undef | 1: temperature, 2: lambda |
| dyntautp | 1.0 | temperature coupling |
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