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,BorCmust 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