| param |
"ff09" |
force field: ff99SB, ff99bsc0, ff03, gaff, GLYCAM_06 |
| 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 |
| dyngamma |
5.0 |
temperature coupling -- collision frequency |
| |
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