Define Options for Common Models
| Model | Define Options |
|---|
| Brooks Go Model for Proteins | NLIST DLIST BGO |
| Brooks Go Model for Proteins with Surface model of Wei and Knotts | NLIST DLIST BGO REST WALL WWALL |
| 3SPN.0 Model for DNA | NLIST DLIST STYPE GOLIK DNA_GOLIK GOBT COULOMB DEBHUCK ZEROAM |
| 3SPN.1 Model for DNA | NLIST DLIST STYPE GOLIK DNA_GOLIK GOBT COULOMB DEBHUCK ZEROAM DRSAM |
| CHARMM19 | NLIST DLIST NEUTRAL COULOMB SASA -RDIE SHIFTF |
| CHARMM22, CHARMM27 with SPME | NLIST DLIST STYPE S14 EWALD SPME |
| Lennard-Jones | NLIST DLIST PRESSURE LJ FCC |
Other Define Options Commonly Used
| Define Option | Description |
|---|
| SEED | Obtain the seed for the random number generator from the system clock. Useful for doing replications. Not usually used if debugging or testing the code. |
| MPI | Used if doing replica exchange or DOS simulations in parallel. |
| TWHAM | Used to output histograms for WHAM analysis when doing replica exchange. Not needed if doing analysis with pyMBAR. |
| XWHAM | Used to output histograms for WHAM analysis when doing umbrella sampling. Not needed if doing analysis with pyMBAR. |
| SCRIPT | Use the script (keyword) format for simul.input instead of the traditional, fixed-line format. |
| ENERGY_FORMAT | Specify the columns to output in energy0.output and ordparam0.output. |
| MKL GAUSS_MKL MKL_ILP64 | Use the Intel Math Kernal Library |
| TLATE | Translate the coordinates each iteration so that the center of mass of the system is at (0,0,0). Useful for movies. |
| TRR | Output a movie file. |
| REST | Add restraints/bonds as defined in rest0.input. Useful for input generation and wall simulations. |
Wall/Surface Options
Several different types of surfaces/walls are available. For each, you must define WALL and one other define option that specifies the type of surface.
| Define Option | Description |
|---|
| NWALL | Neutral wall. A purely-repulsive, short range, Weeks, Chandler, Anderson wall potential. |
| RWALL | A repulsive wall. More long-range than NWALL (Rarely used.) |
| AWALL | An attractive wall (9-3) potential. |
| HWALL | A hard wall. Only used with MC methods. |
| WWALL | Coarse-grain, protein-surface model of Wei and Knotts. Only used with BGO. |
