4. Reference

4.1. 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, B or C must be chosen.

4.1.1. Setting options

curp section

vdw_cutoff_method = atom (default) : Choice[atom]

The method to cut off the van der Waals interaction.

coulomb_method = cutoff (default) : Choice[cutoff]

The method to calculate coulomb interaction.

remove_rotate = yes (default) : Bool

Remove the coordinate and velocity of rotation for the target atoms

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.

decomp_group_current = no (default) : Bool

Flag whether decompose the group current into inside and outside contributions of group region.This option is used for calculating momentum current

coulomb_cutoff_method = atom (default) : Choice[atom]

The method to cut off the coulomb interaction.

group_pair_file = none (default) : File

Path to file to define group pair. If you didn’t given, all of pairs within the targets will be calculated.

target_atoms = 1- (default) : List[String]

The atom list calculated.

potential = amberbase (default) : Choice[amberbase|amber94|amber96|amber99|amber99SB|amber03|amber12SB]

The potential function to calculate the pairwise forces.

vdw_cutoff_length = 99.9 (default) : Float

The cutoff length for the van der Waals interaction.

remove_trans = yes (default) : Bool

Remove the coordinate and velocity of translation for the target atoms

log_frequency = 10 (default) : Int

Log informations will be written out every given steps.

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 parirs, group pairs and both of them will be calculated, respectively.

method = momentum-current (default) : Choice[energy-flux|momentum-current|microcanonical|heat-flux]

The method of calculation.”momentum-current” calculates the stress tensor for systems. “energy-flux” calculates the energy flow 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 hevy atoms covalent to them.”residue” means that the groups are calculated by residue level. If “file” is specified, the groups definition is givenby the group file in input section.

coulomb_cutoff_length = 99.9 (default) : Float

The cutoff length for the coulomb interaction.

dynamics section

trj_format = ascii (default) : Choice[ascii|netcdf]

The format of coordinates and velocities trajectory file.

vels_frequency = 1 (default) : Int

The interval step to write velocity trajectory.

vels_file = none (default) : File

The file path to write out the velocities trajectory. If empty, then don’t write.

integrator = vverlet (default) : Choice[vverlet|leapfrog]

The integrator to want to use with the dynamics.

num_steps = 1 (default) : Int

The number of integration steps.

crds_frequency = 1 (default) : Int

The interval step to write coordinate trajectory.

crds_file = none (default) : File

The file path to write out the coordinates trajectory. If empty, then don’t write.

dt = 0.001 (default) : Float

Time step to advance snapshots to next step, in ps unit.

input section

group_file = group.cfg (default) : File

The group file path to define group.if curp.group_method == file then this definition is used.

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.

format = amber (default) : Choice[presto|amber]

The format of the various files generated by other grograms.

input_amber section

restart_file = none (default) : File

Restart file path.

velocity_file = none (default) : File

Velocity trajectory file path.

target = trajectory (default) : Choice[trajectory|restart]

The target input file to be used.

coordinate_file = none (default) : File

Coordinate trajectory file path.

restart_format = restart (default) : Choice[restart]

The format of restart file.

dump_parameters = no (default) : Bool

Dump the parsed Amber force field parameter set.

velocity_format = ascii (default) : Choice[ascii|netcdf]

The format of velocity file.

topology_file = none (default) : File

Topology file path.

coordinate_format = ascii (default) : Choice[ascii|netcdf]

The format of coordinate file.

output section

energy_decomp = no (default) : Bool

Flag whether decompose the total energy to bonded, coulomb, and van der Waals interaction.

energy_freqency = 0 (default) : Int

The frequency to write the energy information.

format = ascii (default) : Choice[ascii|netcdf]

The format of flux data.

compress = no (default) : Bool

Flag whether compress with gnu zip, then the extension of the file name became “.gz”.

filename = current.dat (default) : File

The file name to output the current or flux information.

frequency = 0 (default) : Int

The frequency to create new file to write the additional file.

energy_compress = yes (default) : Bool

Flag whether compress with gnu zip for energy_file, then the extension of the file name became “.gz”.

energy_file = energy.dat (default) : File

The file path to output the energy information.

output_energy = no (default) : Bool

Flag whether output the energy information or not.

decomp = no (default) : Bool

Flag whether decompose the total current or flux to bonded, coulomb, and van der Waals interaction.

volume section

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]

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.

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_no_hydrogen = no (default) : Bool

Flag to determine whether include hydrogen atomsfor the voronoi calculation.

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.

voronoi_cutoff = 6.0 (default) : Float

The cutoff length that the voronoi calculation finds outneighbour candidate particles.

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.

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.

method = voronoi (default) : Choice[none|vdw|voronoi|outer]

Algorithm to calculate the atomic volumes.

4.2. Input and Output files specification

4.2.1. NetCDF specification of energy 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 that contains total, bond, angle, torsion, improper torsion, coulomb14, vdw14, coulomb and vdw of energy flux if user turn on the keyword, decomp.

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.

4.2.2. 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.

Note

Note that there isn’t ncomponent variable in time-correlation data unlike energy flux data file

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.

4.2.3. Group file specification

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 ]. Then the range of the constituent atoms are provided. You can spacify the range by using - symbol. You can provide multiple data saparated by space, empty line, or tab.

4.3. How to use the CURP tools

4.3.1. curp

usage: compute [-h] [-v] [-s] [--output-conf-default]
               [--output-conf-formatted]
               [input_]

Launch flux or stress tensor computations given a configuration file.

positional arguments:
  input_                Specify input filenames.

optional arguments:
  -h, --help            show this help message and exit
  -v, --vervose         Print out informations.
  -s, --enable-serial   Calculate in serial, don't calculatein parallel.
  --output-conf-default
                        Output the config parameters in ini format with
                        default values.
  --output-conf-formatted
                        Output the config parameters in rest style with
                        default values.

4.3.2. curp

usage: conv-trj [-h] [-crd | -vel] -i TRJ_FILENAME [TRJ_FILENAME ...] -if
                FORMAT [--irange FIRST LAST INTER] [-o TRJ_FILENAME]
                [-of FORMAT] [--orange FIRST LAST INTER] -pf FORMAT -p
                TPL_FILENAME [-nf DIST_FORMAT]
                {convert-only,dry-run,adjust-vel,mask,dist} ...

Various scripts to process and analyze trajectories.

positional arguments:
  {convert-only,dry-run,adjust-vel,mask,dist}
                        Processing command help
    convert-only        Convert the trajectory intoother format.
    dry-run             Do dry-run mode.
    adjust-vel          Adjust time of the velocity trajectory to t from
                        t-dt/2.
    mask                Remove solvent from trajectory.
    dist                Calculate inter-residue distances.

optional arguments:
  -h, --help            show this help message and exit
  -crd                  Specify the format of the trajectory.This argument
                        allows you specify multiple formats.
  -vel                  Specify the format of the trajectory.This argument
                        allows you specify multiple formats.
  -i TRJ_FILENAME [TRJ_FILENAME ...], --input-filenames TRJ_FILENAME [TRJ_FILENAME ...]
                        The trajectory file names.
  -if FORMAT, --input-formats FORMAT
                        Specify the format of the trajectory.This argument
                        allows you specify multiple formats.
  --irange FIRST LAST INTER
                        The trajectory range to process over all trajectory
                        file.
  -o TRJ_FILENAME, --output-filename TRJ_FILENAME
                        The trajectory file name.
  -of FORMAT, --output-format FORMAT
                        The trajectory file format for output.
  --orange FIRST LAST INTER
                        The trajectory range for output
  -pf FORMAT, --topology-format FORMAT
                        Specify the format of the topology file.
  -p TPL_FILENAME, --topology-file TPL_FILENAME
                        Specify the topology file.
  -nf DIST_FORMAT, --name-format DIST_FORMAT
                        Specify the format for representing residue identify.

4.3.3. curp

usage: cal-tc [-h] -o FILE [-a FILE] [-af FORMAT] [-r FIRST LAST INTER]
              [-s SHIFT] [--sample-number NSAMPLE] [-dt DT] [-c COEFFICIENT]
              [-v] [--no-axes]
              FLUX_FILENAME

Calculate transport coefficients from energy flux data.

positional arguments:
  FLUX_FILENAME         The filepath of flux data.

optional arguments:
  -h, --help            show this help message and exit
  -o FILE, --tc-file FILE
                        The filename of tc data.
  -a FILE, --acf-file FILE
                        The filename of acf data.
  -af FORMAT, --acf-file-format FORMAT
                        The file format of acf data.
  -r FIRST LAST INTER, --frame-range FIRST LAST INTER
                        The range of frame; first frame, last frame, interval
                        step.
  -s SHIFT, --average-shift SHIFT
                        The frame to shift for averaging.
  --sample-number NSAMPLE
                        number of sample for one flux data file. Default value
                        is 0 that present to make samples as much as possible
  -dt DT, --dt DT       t of between the neighbour frames. The unit is in ps.
                        Default value is determined by time variable in flux
                        data.
  -c COEFFICIENT, --coefficient COEFFICIENT
                        Multiply acf by given coefficient.
  -v, --vervose         turn on debug mode.
  --no-axes             with this option, scalar flux is handled.

4.3.4. curp

usage: sum-acf [-h] -a FILE [-t FILE] [-c COEFFICIENT] ACF_FILE [ACF_FILE ...]

Average auto-correlation function over the given trajectories

positional arguments:
  ACF_FILE              The filepath of auto-correlation function data.

optional arguments:
  -h, --help            show this help message and exit
  -a FILE, --acf-file FILE
                        The filepath of acf data.
  -t FILE, --tcs-file FILE
                        The filepath of tc time series data.
  -c COEFFICIENT, --coefficient COEFFICIENT
                        Multiply acf by given coefficient.

usage: analyze simplify-tensor [-h] -i FILENAME [-l LABELS] [-s]
                               [fns [fns ...]]

positional arguments:
  fns                   Specify additive filenames. ex.) label_data1,
                        label_data2, ...

optional arguments:
  -h, --help            show this help message and exit
  -i FILENAME, --input-data FILENAME
                        Specify input filename for the stress data.
  -l LABELS, --labels LABELS
                        Specify labels of components to analyze.ex.) -l
                        "total,bond,angle,..."
  -s, --every-snapshot  Specify flag to average the magnitude for every
                        snapshot.

4.3.5. curp

usage: curp graph-een [-h] [-t [TARGETS [TARGETS ...]]]
                      [--forced-output-nodes [FORCE_NODES [FORCE_NODES ...]]]
                      [-p [CLOSE_PAIRS [CLOSE_PAIRS ...]]] [-c CLUSTER_FN]
                      [-n NODE_FN] [--with-one-letter] [-f FIG_FN]
                      [-r THRESHOLD] [-R TPL_THRESHOLD] [--ratio RATIO]
                      [-s GRAPH_SIZE] [--title TITLE] [--direction {LR,TB}]
                      [-I] [--show-negative-values] [--alpha ALPHA]
                      [-lv [LINE_VALUES [LINE_VALUES ...]]]
                      [-lc [LINE_COLORS [LINE_COLORS ...]]]
                      [-lt [LINE_THICKS [LINE_THICKS ...]]]
                      [-lw [LINE_WEIGHTS [LINE_WEIGHTS ...]]]
                      data_fns [data_fns ...]

Show network chart of the energy conductivities.

positional arguments:
  data_fns              Specify filenames.

optional arguments:
  -h, --help            show this help message and exit
  -t [TARGETS [TARGETS ...]], --targets [TARGETS [TARGETS ...]]
                        This option allow you to show only target and thier
                        neighbhor nodes. ex), [-t 1-5], [-t 2-9 15 17], [-t
                        25-].
  --forced-output-nodes [FORCE_NODES [FORCE_NODES ...]]
                        nodes to forcibly show.ex), [-t 1-5], [-t 2-9 15 17],
                        [-t 25-].
  -p [CLOSE_PAIRS [CLOSE_PAIRS ...]], --bring-node-pair-close-together [CLOSE_PAIRS [CLOSE_PAIRS ...]]
                        bring the node pair close together on the EEN
                        graph.ex), 1:2, 3:5, 3:15.
  -c CLUSTER_FN, --cluster-filename CLUSTER_FN
                        Specify a cluster file name.
  -n NODE_FN, --node-style-filename NODE_FN
                        Specify a file name which node style difinitions are
                        written.
  --with-one-letter     use 1 letter representation for amino acid name.
  -f FIG_FN, --output-een-filename FIG_FN
                        Specify a filename to graph EEN.
  -r THRESHOLD, --threshold THRESHOLD
                        threshold value to show nodes on chart figure.
  -R TPL_THRESHOLD, --topology-threshold TPL_THRESHOLD
                        threshold value to define graph topology. If you don't
                        give this parameter, the value of threshold to show
                        nodes will be used.
  --ratio RATIO         ratio of height/width to chart a figure. If '--graph-
                        size is set, this option will be overwrittenby it.
  -s GRAPH_SIZE, --graph-size GRAPH_SIZE
                        The graph size in inch unit. ex) -s '3.4,2.5'
  --title TITLE         Specify the title of the figure.
  --direction {LR,TB}   Specify the kind of the direction.
  -I, --hide-isolated-nodes
                        Hide isolated nodes when appling multiple irEC files.
  --show-negative-values
                        show the nodes pair which have negative values.
  --alpha ALPHA         The transparency value of the background color.
  -lv [LINE_VALUES [LINE_VALUES ...]], --line-values [LINE_VALUES [LINE_VALUES ...]]
                        The threshold values for line attributes. Number of
                        elements in the list must be equal with all line
                        attribute.
  -lc [LINE_COLORS [LINE_COLORS ...]], --line-colors [LINE_COLORS [LINE_COLORS ...]]
                        The colors of line. Number of elements in the list
                        must be equal with all line attribute.
  -lt [LINE_THICKS [LINE_THICKS ...]], --line-thicks [LINE_THICKS [LINE_THICKS ...]]
                        The thickness of line. Number of elements in the list
                        must be equal with all line attribute.
  -lw [LINE_WEIGHTS [LINE_WEIGHTS ...]], --line-weights [LINE_WEIGHTS [LINE_WEIGHTS ...]]
                        The weight of line. Number of elements in the list
                        mustbe equal with all line attribute.

usage: analyze get-ncdata [-h] -r [FRIST:LAST [FRIST:LAST ...]] [-n DATANAME]
                          [-o PREFIX]
                          ACF_FILE

positional arguments:
  ACF_FILE              The filepath of auto-correlation function data.

optional arguments:
  -h, --help            show this help message and exit
  -r [FRIST:LAST [FRIST:LAST ...]], --group-ranges [FRIST:LAST [FRIST:LAST ...]]
                        The pair range list to want to gain.
  -n DATANAME, --dataname DATANAME
                        The name of the netcdf data you want to gain.
  -o PREFIX, --output-prefix PREFIX
                        The prefix of the files to want to write, that
                        includes directory path.

4.4. Contact

Takahisa YAMATO, Dr. Sci.

Graduate School of Science, Nagoya University,

Furo-cho, Chikusa-ku, Nagoya, 4648602, Japan.

Email: yamato@nagoya-u.jp

http://www.tb.phys.nagoya-u.ac.jp/~yamato