AutoSolvateWeb Job Parameters
Available job parameters for the web interface are listed in the following Table.
Parameter |
Description |
Type |
Default Value |
Valid Range |
---|---|---|---|---|
Solute |
The molecule or group of molecules of interest. The file path to solute xyz file is accepted. |
str |
“” |
Not given |
Solvent |
The substance used to mimic the environment surrounding a solute molecule. Available solvents: ‘water’, ‘methanol’, ‘chloroform’, ‘nma’, ‘acetonitrile’. |
str |
‘water’ |
NA |
Charge Method |
Method that determines partial atomic charges. Available methods: ‘bcc’, ‘resp’. Use ‘resp’ (quantum mechanical calculation needed) or ‘bcc’ to estimate partial charges. |
str |
‘resp’ |
‘resp’ only for open-shell system |
Solute Charge |
Net charge of solute, the solvent box will be neutralized with Cl- and Na+ ions. |
int |
0 |
NA |
Solute Spin Multiplicity |
Spin multiplicity of solute. Defined as 2S+1, where S is the total spin quantum number of the molecule. |
int |
1 |
S >= 1 |
Solute Cube Size |
Size of the solvent box for molecular dynamics simulations (in Angstrom). |
int |
54 |
L >=20 |
Dry Run |
Only generate the input files and batch job scripts to run MD programs without executing. |
Bool |
False |
NA |
Temperature |
Temperature in Kelvin to equilibrate in MM or QM/MM calculation. |
int |
300 |
T > 0 |
Pressure |
Pressure in bar to equilibrate during MM NPT step. |
int |
1 |
P > 0 |
MM minimization steps |
Number of steps to minimize the MM potential energy of the system. |
int |
2000 |
n > 0 |
MM heat up steps |
Number of steps to gradually increase the system’s temperature with Langevin dynamics, allowing the simulation to reach a target temperature. Time step: 2 fs/step. Langevin dynamics collision constant: gamma_ln=2.0. Setting it to 0 skips the heating step. |
int |
10000 |
n >= 0 |
MM NPT pressure equilibration steps |
Number of steps to adjust the volume of the simulation box to reach a target constant pressure. Time step: 2 fs/step. Setting it to 0 skips the NPT step. |
int |
300000 |
n >= 0 |
MM NVE production run steps |
Number of steps to evolve the system under constant particle number (N), volume (V), and energy (E) freely without any external constraints. Time step: 2 fs/step. Setting it to 0 skips the NVE step. |
int |
0 |
n >= 0 |
QM/MM minimization steps |
Number of steps to minimize the QM/MM potential energy of the system. |
int |
250 |
n > 0 |
QM/MM heat up steps |
Number of steps to gradually increase the system’s temperature with Langevin dynamics, allowing the simulation to reach a target temperature. Time step: 0.5 fs/step. Langevin dynamics collision constant: gamma_ln=5.0. Setting it to 0 skips the heating step. |
int |
250 |
n >= 0 |
QM/MM NVE production run steps |
Number of steps to evolve the system under constant particle number (N), volume (V), and energy (E) freely without any external constraints. Time step: 0.5 fs/step. Setting it to 0 skips the NVE step. |
int |
0 |
n >= 0 |
QM method |
Treating with high-level quantum mechanical accuracy. Available method: ‘b3lyp’, ‘hf’, ‘case’, ‘dftb’. |
str |
b3lyp |
NA |
Start Frame |
First frame at which to start extracting from the trajectory the microsolvated clusters. |
int |
0 |
n > 0 |
Interval |
Interval in frames at which to extract microsolvated clusters from the trajectory. |
int |
100 |
n > 0 |
Sell thickness |
Solvent shell size for microsolvated clusters in Angstrom, upper limit for minimum solute-solvent distance. |
int |
4 |
n > 0 |