5. Reference
5.1. Specification of curp setting file
This section introduces the description about the setting for the CURP.
The character : after each of the keyword and the value means value
types allowed. For example:
- Int:
integer value.
- Float:
floating value.
- Bool:
boolean value. yes or no.
- File:
specify file path.
- List[type]:
list of the value for the type given in
[and].- Choice[A|B|C]:
A,BorCmust be chosen.
5.1.1. Setting options of curp compute
input section
format = amber (default) : Choice[presto|amber]
The format of the various files generated by other grograms.
first_last_interval = 0 -1 1 (default) : List[Int]
The first, last and interval step to read coordinates and velocities trajectory.
use_simtime = yes (default) : Bool
use the simulation time information in trajectory.
group_file = group.cfg (default) : File
The group file path to define group. If curp.group_method == file then this definition is used.
input_amber section
target = trajectory (default) : Choice[trajectory|restart]
The target input file to be used.
topology_file = none (default) : File
Topology file path.
coordinate_file = none (default) : File
Coordinate trajectory file path.
This option is used when target is set to trajectory.
velocity_file = none (default) : File
Velocity trajectory file path.
This option is used when target is set to trajectory.
restart_file = none (default) : File
Restart file path.
This option is used when target is set to restart.
coordinate_format = ascii (default) : Choice[ascii|netcdf]
The format of coordinate file.
This option is used when target is set to trajectory.
velocity_format = ascii (default) : Choice[ascii|netcdf]
The format of velocity file.
This option is used when target is set to trajectory.
restart_format = restart (default) : Choice[restart]
The format of restart file.
This option is used when target is set to restart.
dump_parameters = no (default) : Bool
Dump the parsed Amber force field parameter set.
volume section
Note
This section is used for calculating the stress tensor.
method = voronoi (default) : Choice[none|vdw|voronoi|outer]
Algorithm to calculate the atomic volumes.
atomic_trajectory_file = none (default) : File
Atomic volumes trajectory file path for outer method.
group_trajectory_file = none (default) : File
Group volumes trajectory file path for outer method.
voronoi_cutoff = 6.0 (default) : Float
The cutoff length that the voronoi calculation finds out neighbour candidate particles.
voronoi_no_hydrogen = no (default) : Bool
Flag to determine whether to include hydrogen atoms for the voronoi calculation.
voronoi_solvation = none (default) : Choice[none|RANDOM20]
The kind of solvation system to sink the target system in vacuum for the voronoi method. The density value of the water under NPT ensemble is 0.99651 [g/cm^3] at 27 [Kelvin]
voronoi_probe_length = 2.4 (default) : Float
The probe length of the solvation for the voronoi method.The water molecules within the probe length from the system are removed.
voronoi_output_solvation_file = none (default) : File
The file path to write out the solvation pdb data in the case of voronoi_solvation == “none”. If the file path is not given, writing out is not performed.
output_volume_file = none (default) : File
The file path to write out the atomic volumes trajectory. If this value is not given, writing out is not performed. The file written by this option can be used in the options,atomic_trajectory_file.
output_gvolume_file = none (default) : File
The file path to write out the group volumes trajectory. If this value is not given, writing out is not performed. The file written by this option can be used in the optionsgroup_trajectory_file.
curp section
Warning
The parameters “coulomb_method” is deprecated in version 3.0. Please use “nonbonded_method” instead.
potential = amberbase (default) : Choice[amberbase|amber94|amber96|amber99|amber99SB|amber03|amber12SB|amber19SB]
The potential function to calculate the pairwise forces.
If you use the amber19SB, the CMAP term is calculated.
target_atoms = 1- (default) : List[String]
The atom list calculated.
method = momentum-current (default) : Choice[energy-flux|momentum-current|microcanonical|heat-flux]
Warning
The “momentum-current” and “microcanonical” methods are not supported on and after version 1.3.
The method of calculation. “momentum-current” calculates the stress tensor for systems. “energy-flux” calculates the energy flow for systems. “microcanonical” calculates the microcanonical current for systems. “heat-flux” calculates the heat flux for systems. dynamics is mainly used to verify the validity of the CURP program numerically, so its implementation is very simple
group_method = none (default) : Choice[united|residue|file|none]
The method to construct the group. “united” means that hydrogen atoms are included in heavy atoms covalent to them. “residue” means that the groups are calculated by residue level. If “file” is specified, the groups definition is given by the group file in input section.
flux_grain = group (default) : Choice[atom|group|both]
The grain to calculate the flux. “atom”, “group” and “both” values mean that the flux for atom pairs, group pairs and both of them will be calculated, respectively.
Warning
When nonbonded_method is set to treecode, only “group” value is available. If other two values are given, the error will be raised.
decomp_group_current = no (default) : Bool
Flag whether to decompose the group current into inside and outside contributions of group region. This option is used for calculating momentum current.
group_pair_file = none (default) : File
Path to file to define group pairs. If this is not given, all of pairs within the targets will be calculated.
This option is used when flux_grain is set to group or both.
nonbonded_method = cutoff (default) : Choice[cutoff|treecode]
Note
New option in version 3.0.
The method to calculate coulomb interaction.
“cutoff”: particle-particle nonbonded interaction are evaluated.
“treecode”: particle-cell (particle-particle) coulombic interactions are evaluated for the distant (near) particle pairs, while van der Waals interaction for the distant particle pairs are neglected.
coulomb_cutoff_method = atom (default) : Choice[atom]
The method to cut off the coulomb interaction.
This option is used when nonbonded_method is set to cutoff.
coulomb_cutoff_length = 99.9 (default) : Float
The cutoff length for the coulomb interaction.
The unit is in Angstrom. This option is used when nonbonded_method is set to cutoff.
treecode_cell_contains = 50 (default) : Float
Note
New option in version 3.0.
The max number of atoms that a cell can contain.
treecode_direct_parm = 0.02 (default) : Float
Note
New option in version 3.0.
The parameter that is used to decide whether to perform direct nonbonded calculation.
This option is used when nonbonded_method is set to treecode.
treecode_cutoff_length = 12.0 (default) : Float
Note
New option in version 3.0.
The cutoff length for the treecode calculation. The unit is in Angstrom.
This option is used when nonbonded_method is set to treecode.
vdw_cutoff_method = atom (default) : Choice[atom]
The method to cut off the van der Waals interaction.
This option is used when nonbonded_method is set to cutoff.
vdw_cutoff_length = 99.9 (default) : Float
The cutoff length for the van der Waals interaction.
This option is used when nonbonded_method is set to cutoff.
enable_inverse_pair = no (default) : Bool
Calculate and write out inverse pairs j <- i for flux adding normal group pairs: i <- j. This option is used in the case for calculating energy flux(method == energy-flux).
remove_trans = yes (default) : Bool
Remove the coordinate and velocity of translation for the target atoms
remove_rotate = yes (default) : Bool
Remove the coordinate and velocity of rotation for the target atoms
log_frequency = 10 (default) : Int
Log informations will be written out every given steps.
table_length_limit = 0 (default) : Int
Note
New option in version 3.0.
The limit of nonbonded interaction table length. If this value is not given(0), the length is determined by “10 * (the max atom number in the system)”. If a non-zero value is given, the limit of the table length is determined by the given value.
If the number of pairs exceeds the limit, the error will be raised.
dynamics section
Note
This section is used for performing microcanonical simulation(method in curp section is microcanonical).
integrator = vverlet (default) : Choice[vverlet|leapfrog]
The integrator to want to use with the dynamics.
dt = 0.001 (default) : Float
Time step to advance snapshots to next step, in ps unit.
num_steps = 1 (default) : Int
The number of integration steps.
crds_file = none (default) : File
The file path to write out the coordinates trajectory. If empty, then don’t write.
vels_file = none (default) : File
The file path to write out the velocities trajectory. If empty, then don’t write.
crds_frequency = 1 (default) : Int
The interval step to write coordinate trajectory.
vels_frequency = 1 (default) : Int
The interval step to write velocity trajectory.
trj_format = ascii (default) : Choice[ascii|netcdf]
The format of coordinates and velocities trajectory file.
output section
filename = current.dat (default) : File
The file name to output the current or flux information.
format = ascii (default) : Choice[ascii|netcdf]
The format of flux data.
decomp = no (default) : Bool
Flag whether to decompose the total current or flux to bonded, coulomb, and van der Waals interaction.
frequency = 0 (default) : Int
The frequency to create new file to write the additional file.
compress = no (default) : Bool
Flag whether to compress with gnu zip, then the extension of the file name became “.gz”.
Warning
The parameters below are not active in version 3.0, but will be active in the future version.
output_energy = no (default) : Bool
Flag whether to output the energy information or not.
energy_file = energy.dat (default) : File
The file path to output the energy information.
energy_decomp = no (default) : Bool
Flag whether to decompose the total energy to bonded, coulomb, and van der Waals interaction.
energy_freqency = 0 (default) : Int
The frequency to write the energy information.
energy_compress = yes (default) : Bool
Flag whether to compress with gnu zip for energy_file, then the extension of the file name became “.gz”.
5.2. Input and Output files specification
5.2.1. NetCDF specification of flux data file
Please visit NetCDF website to use NetCDF format file for more information.
dimensions
- nframe
The number of frames. This dimension is unlimited.
- npair
The number of group pairs.
- ncomponent
The number of components.
Note
The contents of the ncomponent is determined by the setting of output.decomp, curp.potential and curp.nonbonded_method in the setting file.
output.decomp
curp.potential
curp.nonbonded_method
ncomponent
no
(anything)
(anything)
1 (total)
yes
- (anything
except “amber19SB”)
“cutoff”
- 9 (total, bond, angle, torsion, improper,
coulomb14, vdw14, coulomb, vdw)
yes
“amber19SB”
“cutoff”
- 10(total, bond, angle, torsion, improper,
cmap, coulomb14, vdw14, coulomb, vdw)
yes
- (anything
except “amber19SB”)
“treecode”
- 8(total, bond, angle, torsion, improper,
coulomb14, vdw14, nonbonded)
yes
“amber19SB”
“treecode”
- 9(total, bond, angle, torsion, improper,
cmap, coulomb14, vdw14, nonbonded)
- nchar
The number of character array.
variables
- time(nframe)
Array of the calculated time.
- donors(npair, nchar)
Array of donor name at i:sup:th pair.
- acceptors(npair, nchar)
Array of acceptor name at i:sup:th pair.
- components(ncomponent, nchar)
Array of component names
- flux(nframe, npair, ncomponent)
Array flux data.
5.2.2. NetCDF specification of time-correlation data
Please visit NetCDF website to use NetCDF format file for more information.
dimensions
- nframe
The number of frames.
- npair
The number of group pairs. This dimension is unlimited.
- ncomponent
The number of components.
Note
The contents of the ncomponent is determined by the setting of output.decomp, curp.potential and curp.nonbonded_method in the setting file. See “NetCDF specification of flux data file” section for more details.
- nchar
The number of character array.
variables
- time(nframe)
Array of the calculated time.
- donors(npair, nchar)
Array of donor name at i:sup:th pair.
- acceptors(npair, nchar)
Array of acceptor name at i:sup:th pair.
- acf(npair, nframe)
Array flux data.
5.2.3. Group file specification
Atom group file
[GROUP1]
(the array of atom indices in "GROUP1")
[GROUP2]
(the array of atom indices in "GROUP2")
...
For example, you can separate the main chain and the side chain parts by using the following specification:
[01_ALA_M]
1-6 11-12
[01_ALA_S]
7-10
[02_ALA_M]
13-16 21-22
[02_ALA_S]
17-20
[03_ALA_M]
23-26 31-33
[03_ALA_S]
27-30
The group names are surrounded by [ and ]. Each group name should be unique. Then the range of the constituent atoms are provided. You can spacify the range by using - symbol. You can provide multiple data separated by space, empty line, or tab. Each atom can belong to only one group. If an atom belongs to multiple groups, the error will be raised.
Group pair file
[GROUP1]
GROUP1 GROUP2 GROUP3 ...
[GROUP2]
GROUP2 GROUP3 ...
When you want to calculate the flux from “GROUP2” to “GROUP1”, you can specify the group pair as “[GROUP1]” and “GROUP2” in the group pair file.
For example, when you use the atom group file above, you can specify the group pairs as follows:
[01_ALA_M]
01_ALA_S 02_ALA_M
[01_ALA_S]
03_ALA_S 02_ALA_S 03_ALA_M
[02_ALA_M]
03_ALA_S 02_ALA_S 03_ALA_M
Here the first and second lines mean that the two fluxes are calculated and written: flux from 01_ALA_S to 01_ALA_M and the flux from 02_ALA_M to 01_ALA_M.
You cannot specify the same group pair more than once. If you specify the same group pair more than once, the error will be raised.
In the atom group file, the “GROUP1” should be defined earlier than the “GROUP2” when you perform flux calculation from “GROUP2” to “GROUP1”. In the case of the example above, you cannot specify “01_ALA_M” in the fifth line because “01_ALA_M” is defined earlier than “01_ALA_S” in the atom group file. If the “GROUP1” is defined later than the “GROUP2”, the error will be raised.
The flux calculation of group pair “GROUP1” and “GROUP1” is available for the intra-group thermal conductivity calculation. (Note that you cannot calculate the intra-group energy flux because the energy flux should be defined as the flux between different groups.)
5.3. Contact
Takahisa YAMATO, Dr. Sci.
Graduate School of Science, Nagoya University,
Furo-cho, Chikusa-ku, Nagoya, 4648602, Japan.
Email: yamato@nagoya-u.jp