AutoSolvateWeb Job Parameters

Available job parameters for the web interface are listed in the following Table.

General Parameter

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