4. All Option Keywords

Here, we describe all option keywords in ABPolymer input file. You can find an input file containing all options here: Input File.

4.1. charmm

scaling14

Value	A real number
Default	1.0

Define the scaling factor for electrostatic interactions of 1-4 term.

rcutoff

Value	A real number
Default	15.0

Define the distance in Angstrom to cutoff non-bonded interactions.

If rswitch is larger than rcutoff, switching function will not be used and no cutoff is applied on long range forces.

rswitch

Value	A real number
Default	10.0

Define the distance in Angstrom to activate switching function.

If rswitch is larger than rcutoff, switching function will not be used and no cutoff is applied on long range forces.

4.2. opt

This option controls the geometry optimization details.

num_steps

Value	An integer
Default	1000

The maximum number of geometry optimization steps.

epsilon

Value	A real number
Default	1.E-2

The convergence condition. If the ratio of gradient norm to coordinate norm is less than epsilon, then the optimization is assumed to be converged.

4.3. md

This option controls the NVT molecular dynamics (MD) simulation details.

dt

Value	A real number
Default	0.0005

The time step in ps. For systems not containing hydrogen atoms, dt can be set to 0.001 ps.

num_steps

Value	An integer
Default	10000

The number of MD steps to be run.

output_freq

Value	An integer
Default	100

The number of steps that MD information is output. The trajectory will be output to disk.

temp

Value	A real number
Default	300

Define the target temperature for NVT simulation.

temp_nhc_length

Value	An integer
Default	5

The length of Nose-Hoover chain to control the temperature. Usually an integer larger than 2 is enough.

temp_nhc_tau

Value	A real number
Default	0.05

The time-constant of Nose-Hoover chain to control the temperature in ps.

4.4. grow

This option controls the amorphous material growth details.

dir_fn

Value	A directory name
Default	x

The folder to store all intermediate files during the simulation. This directory should have NOT already existed, otherwise ABPolymer will raise an error like Cannot create directory "x" to save intermediates.

num_steps

Value	An integer
Default	-1

If a positive number is given, the growing will be performed for num_steps steps. If -1 is given, the growing will stop when all units are depleted.

r_intra

Value	A real number
Default	4

Define the distance in Angstrom at which an intramolecular bond may form.

If 2 reactive sites of the same molecule are within this distance, a bond MAY form between them. So, if you set it to a negative value like -4, no intramolecular polymerization will occur.

md_freq

Value	An integer
Default	10

The frequency to do MD information. For example, if you set md_freq to 10, then every 10 growing steps, an NVT MD (controlled by the md block) will be performed.

4.5. unit

This option gives the components of the amorphous material. A typical input is:

unit
    paf1.xyz           100
    myunits/paf80.xyz  10
end

This means that the amorphous material contains 100 monomers defined by paf1.xyz and 10 monomers defined by myunits/paf80.xyz. The order does not matter, since ABPolymer will grow with a random monomer in each step.

For details of preparing monomer file *.xyz, see Monomer File Preparation.