# nwARGOS input

Input file format

The input file project_id.inp determines the type of calculation to be performed. Details of the calculation are given in keyworded format.

Input file keywords

Keywords need to be given exactly as given below. Numeric values are in free format. Keywords recognized include

`#`
Any card in the input file that starts with the number sign (#) is treated as a comment, and ignored.

``
Any card in the input file that starts with a space is treated as a comment, and ignored.

`Title`
Three title cards (a) and one with date and time (2a10) are read.

`Task SP`
Identifies that a single point energy evaluation is to be done using parameters from set 1. This card cancels any previous `Task` cards in the input deck.

`Task SP set 2`
Identifies that a single point energy evaluation is to be done using parameters from set 2. This card cancels any previous `Task` cards in the input deck.

`Task SP set 3`
Identifies that a single point energy evaluation is to be done using parameters from set 3. This card cancels any previous `Task` cards in the input deck.

`Task MD`
Identifies that a molecular dynamics simulation is to be carried out using parameters from set 1. This card cancels any previous `Task` cards in the input deck.

`Task MD set 2`
Identifies that a molecular dynamics simulation is to be carried out using parameters from set 2. This card cancels any previous `Task` cards in the input deck.

`Task MD set 3`
Identifies that a molecular dynamics simulation is to be carried out using parameters from set 3. This card cancels any previous `Task` cards in the input deck.

`Task EM`
Identifies that an energy minimization is to be performed out using parameters from set 1. This card cancels any previous `Task` cards in the input deck.

`Task EM set 2`
Identifies that an energy minimization is to be performed out using parameters from set 2. This card cancels any previous `Task` cards in the input deck.

`Task EM set 3`
Identifies that an energy minimization is to be performed out using parameters from set 3. This card cancels any previous `Task` cards in the input deck.

`Task MCTI`
Identifies that a multiconfiguration thermodynamic integration calculation will be carried out. This card cancels any previous `Task` cards in the input deck.

`Start time` rvalue
This keywords sets the initial time for molecular dynamics simulations to rvalue. The default value is 0.000 ps.

`Time step` rvalue
This keywords sets the time-step for molecular dynamics simulations to rvalue. The default value is 0.001 ps.

`SD iterations` ivalue
This keywords sets the maximum number of steepest descent iterations for energy minimization calculations to ivalue. The default value is 100.

`SD initial step` rvalue
This keywords sets the initial step size for steepest descent energy minimization calculations to rvalue. The default value is 0.010 nm.

`CG iterations` ivalue
This keywords sets the maximum number of conjugate gradient iterations for energy minimization calculations to ivalue. The default value is 0.

`CG cycles` ivalue
This keywords sets the conjugate gradient refresh cycle for energy minimization calculations to ivalue. The default value is 0.

`MCTI windows total` ivalue
This keywords sets the total number of multiconfiguration thermodynamic integration steps for a free energy calculations to ivalue. The default value is 21.

`MCTI windows` ivalue
This keywords sets the number of multiconfiguration thermodynamic integration steps for a free energy calculation that will be done in this run to ivalue. The default value is equal to the total number of integration steps.

`MCTI separation shifted scaling delta` rvalue
This keywords sets the separation shifted scaling distance parameter delta to rvalue. The default, and recommended, value is 0.075 nm^2.

`MCTI separation shifted scaling`
This keyword activates separation shifted scaling in MCTI free energy calculations. Per default separation shifted scaling is turned off.

`Print topology`
This keyword activates printing of the topology, for both solvent and solute. Per default the topology is not printed.

`Print topology solvent`
This keyword activates printing of the solvent topology. Per default the solvent topology is not printed.

`Print topology solute`
This keyword activates printing of the solute topology. Per default the solute topology is not printed.

`Print step`
This keyword activates printing of more detailed information at each printed time step. Per default only total system energies are printed.

`Print step energies`
This keyword activates printing of even more detailed energy information at each printed time step. Per default only total system energies are printed.

`Print timing analysis all nodes`
This keyword activates printing at the end of the run the timing analysis of all nodes. Per default only the timing analysis of node 0 is printed.

`Equilibration steps` ivalue
This keyword sets the number of equilibration steps in an MD run or in an MCTI window to ivalue. The default number of equilibration steps is 0.

`Data gathering steps` ivalue
This keyword sets the number of data gathering steps in an MD run or in an MCTI window to ivalue. The default number of data gathering steps is 100.

`Cutoff radius WW SR` rvalue

`Cutoff radius WW LR` rvalue

`Cutoff radius SW SR` rvalue

`Cutoff radius WS SR` rvalue

`Cutoff radius SW LR` rvalue

`Cutoff radius WS LR` rvalue

`Cutoff radius SS SR` rvalue

`Cutoff radius SS LR` rvalue

`Cutoff radius SR` rvalue
This keyword sets all short-range cutoff radii to rvalue. The default value is 0.9 nm.

`Cutoff radius LR` rvalue
This keyword sets all long-range cutoff radii to rvalue. The default value is 0.9 nm.

`Cutoff radius` rvalue
This keyword sets all cutoff radii to rvalue. The default value is 0.9 nm.

`SHAKE iterations W` ivalue
This keywrods sets the maximum number of solvent SHAKE iterations to ivalue. The default is 100.

`SHAKE iterations S` ivalue
This keywrods sets the maximum number of solute SHAKE iterations to ivalue. The default is 100.

`SHAKE iterations` ivalue
This keywrods sets the maximum number of SHAKE iterations to ivalue for both solvent and solute. The default is 100.

`SHAKE tolerance W` rvalue
This keyword sets the solvent SHAKE tolerance to rvalue. The default value is 0.001 nm.

`SHAKE tolerance S` rvalue
This keyword sets the solute SHAKE tolerance to rvalue. The default value is 0.001 nm.

`SHAKE tolerance` rvalue
This keyword sets the SHAKE tolerance to rvalue for both solvent and solute. The default value is 0.001 nm.

`Binary recording`
This keyword enables binary recording. Per default all recording files are ASCII formatted files.

`Frequency centering solute` ivalue
This keyword sets the frequency of centering the solute center of geometry. The default frequency is 0.

`Frequency update pairlists` ivalue
This keyword sets the frequency of updating the pairlists. The default frequency is 1.

`Frequency update LR forces` ivalue
This keyword sets the frequency of updating the long range forces. The default frequency is 1.

`Frequency recording output` ivalue
This keyword sets the frequency of recording selected information of a MD step, EM iteration or MCTI integration step to the output file to ivalue. The default frequency is 1.

`Frequency recording statistics` ivalue
This keyword sets the frequency of recording statistical information accumulated during MD and MCTI calculations to output to ivalue. The default frequency is 1.

`Frequency recording restart` ivalue
This keyword sets the frequency of recording the restart file to ivalue. The default value is 0.

`Frequency recording free energy` ivalue
This keyword sets the frequency of recording the free energy data to file to ivalue, during MCTI calculations. The default value is 1.

`Load balance box size`
This keyword specifies that loadbalancing is to be done based on resizing of sub-boxes. Per default no load balancing is done.

`Load balance box pairs`
This keyword specifies that loadbalancing is to be done based on redistribution of internode sub-box pairs. Per default no load balancing is done.

`Constant pressure` rvalue
This keyword specifies that the simulation is to be done for a constant pressure of rvalue Pa. Per default the simulation is at constant volume.

`Pressure relaxation time` rvalue
This keyword sets the pressure relation time to rvalue ps. The default value is 0.5 ps.

`Compressebility` rvalue
This keyword sets the compressebility of the molecular system to rvalue ps. The default value is 4.53 10^10.

`Constant temperature WS` rvalue
This keyword specifies that the simulation is to be done for a constant temperature of rvalue K, in which the scaling is done separately for solvent and solute. Per default the simulation is at constant energy.

`Constant temperature` rvalue
This keyword specifies that the simulation is to be done for a constant temperature of rvalue K, in which the scaling is done for the complete molecular system. Per default the simulation is at constant energy.

`Temperature relaxation time W` rvalue
This keyword sets the solvent temperature relation time to rvalue ps. The default value is 0.1 ps.

`Temperature relaxation time S` rvalue
This keyword sets the solute temperature relation time to rvalue ps. The default value is 0.1 ps.

`Temperature relaxation time` rvalue
This keyword sets the temperature relation time to rvalue ps for both solvent and solute. The default value is 0.1 ps.

`Velocity reassignment frequency WS` ivalue
The keyword sets the velocity reassignment frequency to ivalue for solvent and solute to separately obtain the reassigment temperature. The default value is 0.

`Velocity reassignment frequency` ivalue
The keyword sets the velocity reassignment frequency to ivalue for the molecular system to obtain the reassigment temperature. The default value is 0.

`Velocity reassignment temperature` rvalue
This keyword sets the velocity reassignment temperature. The default value is 298.15 K.