Action: VES_OUTPUT_TARGET_DISTRIBUTION

Module	ves
Description	Usage
Output target distribution to file.

Details and examples

Output target distribution to file.

This action can be used to output target distributions to a grid file, for example to see how they look like before using them in a VES bias. This action only support static target distributions.

This action is normally used through the driver.

Examples

In the following input we define a target distribution that is uniform for argument 1 and a Gaussian for argument 2 and then output it to a file called targetdist-1.data.

Click on the labels of the actions for more information on what each action computes

t1_1: TD_UNIFORMUniform target distribution (static). More details  MINIMAThe minimum of the intervals where the target distribution is taken as uniform=-4.0  MAXIMAThe maximum of the intervals where the target distribution is taken as uniform=+4.0
The TD_UNIFORM action with label t1_1 calculates somethingt1_2: TD_GAUSSIANTarget distribution given by a sum of Gaussian kernels (static). More details  CENTER1The centers of the Gaussian distributions=-2.0  SIGMA1The standard deviations of the Gaussian distributions=0.5
The TD_GAUSSIAN action with label t1_2 calculates somethingt1: TD_PRODUCT_DISTRIBUTIONTarget distribution given by a separable product of one-dimensional distributions (static or dynamic). More details  DISTRIBUTIONSLabels of the one-dimensional target distribution actions for each argument to be used in the product distribution=t1_1,t1_2

The TD_PRODUCT_DISTRIBUTION action with label t1 calculates somethingVES_OUTPUT_TARGET_DISTRIBUTIONOutput target distribution to file. More details ...
 GRID_MINthe lower bounds for the grid=-4.0,-4.0
 GRID_MAXthe upper bounds for the grid=+4.0,+4.0
 GRID_BINSthe number of bins used for the grid=100,100
 TARGET_DISTRIBUTIONthe target distribution to be used=t1
 TARGETDIST_FILEfilename of the file for writing the target distribution=targetdist-1.data
 LOG_TARGETDIST_FILEfilename of the file for writing the log of the target distribution=targetdist-1.log.data
 FMT_GRIDSthe numerical format of the target distribution grids written to file=%11.6f
... VES_OUTPUT_TARGET_DISTRIBUTION

This input should be run through the driver by using a command similar to the following one where the trajectory/configuration file configuration.gro is needed to trick the code to exit correctly.

plumed driveranalyze trajectories with plumed This action has hidden defaults. More details --plumed specify the name of the plumed input file plumed.dat --igrothe trajectory in gro format configuration.gro

The driver action with label plumed calculates somethingplumed driveranalyze trajectories with plumed This action uses the defaults shown here. More details --plumed specify the name of the plumed input file plumed.dat --igrothe trajectory in gro format configuration.gro
 --timestep the timestep that was used in the calculation that produced this trajectory in picoseconds 1.0 --trajectory-stride the frequency with which frames were output to this trajectory during the simulation (0 means that the number of the step is read from the trajectory file, currently working only for xtc/trr files read with --ixtc/--trr) 1 --multi set number of replicas for multi environment (needs MPI) 0 --dump-forces-fmt the format to use to dump the forces %%f 

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
GRID_MIN	compulsory	none	the lower bounds for the grid
GRID_MAX	compulsory	none	the upper bounds for the grid
GRID_BINS	compulsory	none	the number of bins used for the grid
TARGETDIST_FILE	compulsory	none	filename of the file for writing the target distribution
TARGET_DISTRIBUTION	compulsory	none	the target distribution to be used
GRID_PERIODICITYThis keyword do not have examples	optional	not used	specify if the individual arguments should be made periodic (YES) or not (NO)
LOG_TARGETDIST_FILE	optional	not used	filename of the file for writing the log of the target distribution
FMT_GRIDS	optional	not used	the numerical format of the target distribution grids written to file
DO_1D_PROJECTIONSThis keyword do not have examples	optional	false	Also output the one-dimensional marginal distributions for multi-dimensional target distribution