PLUMED-NEST

Project ID: plumID:19.080
Source: ohco2/symm-fes/plumed.inp
Originally used with PLUMED version: 2.4.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,3 LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 R_0The r_0 parameter of the switching function=1.75 NN The n parameter of the switching function =4 LABELa label for the action so that its output can be referenced in the input to other actions=coordThe COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Type   
 Description  
coord
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 R_0The r_0 parameter of the switching function=1.75 NN The n parameter of the switching function =4 LABELa label for the action so that its output can be referenced in the input to other actions=coord  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=4,3,5 LABELa label for the action so that its output can be referenced in the input to other actions=angThe ANGLE action with label ang calculates the following quantities:
 Quantity   
 Type   
 Description  
ang
scalar
the ANGLE involving these atoms

COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=dis1The COORDINATION action with label dis1 calculates the following quantities:
 Quantity   
 Type   
 Description  
dis1
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=dis1  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=dis2The COORDINATION action with label dis2 calculates the following quantities:
 Quantity   
 Type   
 Description  
dis2
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5 R_0The r_0 parameter of the switching function=1.15 NN The n parameter of the switching function =12 LABELa label for the action so that its output can be referenced in the input to other actions=dis2  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=dis1,dis2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=nmThe COMBINE action with label nm calculates the following quantities:
 Quantity   
 Type   
 Description  
nm
scalar
a linear compbination

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=100.0 LABELa label for the action so that its output can be referenced in the input to other actions=constrain1The UPPER_WALLS action with label constrain1 calculates the following quantities:
 Quantity   
 Type   
 Description  
constrain1.bias
scalar
the instantaneous value of the bias potential
constrain1.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=1.3 KAPPAthe force constant for the wall=500.0 LABELa label for the action so that its output can be referenced in the input to other actions=constrain2The UPPER_WALLS action with label constrain2 calculates the following quantities:
 Quantity   
 Type   
 Description  
constrain2.bias
scalar
the instantaneous value of the bias potential
constrain2.force2
scalar
the instantaneous value of the squared force due to this bias potential
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=nm FILEthe name of the file containing the external potential=extbias LABELa label for the action so that its output can be referenced in the input to other actions=externalThe EXTERNAL action with label external calculates the following quantities:
 Quantity   
 Type   
 Description  
external.bias
scalar
the instantaneous value of the bias potential
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=nm FILEthe name of the file containing the external potential=extbias LABELa label for the action so that its output can be referenced in the input to other actions=external  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0

bf1: BF_CHEBYSHEVChebyshev polynomial basis functions. More details MINIMUMThe minimum of the interval on which the basis functions are defined=1 MAXIMUMThe maximum of the interval on which the basis functions are defined=3.0 ORDERThe order of the basis function expansion=48

The BF_CHEBYSHEV action with label bf1 calculates somethingtd: TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More details BIASFACTORThe bias factor used for the well-tempered distribution=30

# Expansion

The TD_WELLTEMPERED action with label td calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
 ARGthe labels of the scalars on which the bias will act=d1
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
 GRID_BINSthe number of bins used for the grid=400
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
the instantaneous value of the bias potential
b1.force2
scalar
the instantaneous value of the squared force due to this bias potential.
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
 ARGthe labels of the scalars on which the bias will act=d1
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=300
 GRID_BINSthe number of bins used for the grid=400
 TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
 LABELa label for the action so that its output can be referenced in the input to other actions=b1
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

# Optimization algorithm

OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=4000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.5
  FES_OUTPUThow often the FES(s) should be written out to file=10
  BIAS_OUTPUThow often the bias(es) should be written out to file=1000
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=10
  COEFFS_OUTPUT how often the coefficients should be written to file=1
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=5
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:
 Quantity   
 Description  
o1.value
a scalarOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details ...
  BIASthe label of the VES bias to be optimized=b1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=4000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  STEPSIZEthe step size used for the optimization=0.5
  FES_OUTPUThow often the FES(s) should be written out to file=10
  BIAS_OUTPUThow often the bias(es) should be written out to file=1000
  FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=10
  COEFFS_OUTPUT how often the coefficients should be written to file=1
  TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization=5
 COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD


FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=200
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,coord,ang,b1.bias STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar