PLUMED-NEST-TEST-SITE

Project ID: plumID:20.024
Source: Hydrobromination/static_bias/plumed.dat
Originally used with PLUMED version: 2.7
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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../GAMBES.cpp
The LOAD action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs

d1:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethings1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5 COEFFICIENTS the coefficients of the arguments in your function=-0.523,0.726,0.401,-0.029,-0.193 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label s1 calculates the following quantities:
 Quantity   
 Description  
s1.value
a linear compbinations2: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5 COEFFICIENTS the coefficients of the arguments in your function=0.573,-0.339,-0.183,-0.636,-0.345 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label s2 calculates the following quantities:
 Quantity   
 Description  
s2.value
a linear compbinationGAMBESThis action is not part of PLUMED and was included by using a LOAD command More details ...
  ARG=d1,d2,d3,d4,d5
  NSTATES=3
  FILENAME=gdist_n
  PACE=500
  LABEL=ext
  BIAS_CUTOFF
  CUTOFF=150
  LAMBDA=0.01 
  TEMPERATURE=300
  STATIC_BIAS
  STATIC_FACTORS=1,4000,1.0006
... GAMBES

uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5 ATthe positions of the wall=3.0,3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=150.0,150.0,150.0,150.0,150.0  

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialH1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3,4
The GROUP action with label H1 calculates somethingH2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=7,8,9
The GROUP action with label H2 calculates somethingH: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=11
The GROUP action with label H calculates somethingC_end: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1,5
The GROUP action with label C_end calculates somethingC_mid: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2
The GROUP action with label C_mid calculates somethingBr: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=10
The GROUP action with label Br calculates somethingCe1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1
The GROUP action with label Ce1 calculates somethingCe2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5
The GROUP action with label Ce2 calculates somethingH_all: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3,4,6,7,8,9,11

The GROUP action with label H_all calculates somethingdCe1H1: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Ce1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H1 HIGHEST this flag allows you to recover the highest of these variables NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dCe1H1 calculates the following quantities:
 Quantity   
 Description  
dCe1H1.highest
the largest of the colvars
dCe1H1.value
the DISTANCES between the each pair of atoms that were specifieddCe2H2: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Ce2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H2 HIGHEST this flag allows you to recover the highest of these variables NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dCe2H2 calculates the following quantities:
 Quantity   
 Description  
dCe2H2.highest
the largest of the colvars
dCe2H2.value
the DISTANCES between the each pair of atoms that were specifieddCmH1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dCmH1 calculates the following quantities:
 Quantity   
 Description  
dCmH1.value
the DISTANCE between this pair of atomsdHH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H_all GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H_all MINcalculate the minimum value={BETA=20} NOPBC ignore the periodic boundary conditions when calculating distances

The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum colvar
dHH.value
the DISTANCES between the each pair of atoms that were specifiedd13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomswallCe1H1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d13,d14 ATthe positions of the wall=1.4,1.4 KAPPAthe force constant for the wall=150.0,150.0 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2

The UPPER_WALLS action with label wallCe1H1 calculates the following quantities:
 Quantity   
 Description  
wallCe1H1.bias
the instantaneous value of the bias potential
wallCe1H1.force2
the instantaneous value of the squared force due to this bias potentiald57: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d57 calculates the following quantities:
 Quantity   
 Description  
d57.value
the DISTANCE between this pair of atomsd58: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,8 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d58 calculates the following quantities:
 Quantity   
 Description  
d58.value
the DISTANCE between this pair of atomsd59: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d59 calculates the following quantities:
 Quantity   
 Description  
d59.value
the DISTANCE between this pair of atomswallCe2H2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d57,d58,d59 ATthe positions of the wall=1.4,1.4,1.4 KAPPAthe force constant for the wall=150.0,150.0,150.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1.0,1.0,1.0 OFFSET the offset for the start of the wall=0.2,0.2,0.2
The UPPER_WALLS action with label wallCe2H2 calculates the following quantities:
 Quantity   
 Description  
wallCe2H2.bias
the instantaneous value of the bias potential
wallCe2H2.force2
the instantaneous value of the squared force due to this bias potentialwallCmH1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dCmH1 ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 OFFSET the offset for the start of the wall=0.2
The UPPER_WALLS action with label wallCmH1 calculates the following quantities:
 Quantity   
 Description  
wallCmH1.bias
the instantaneous value of the bias potential
wallCmH1.force2
the instantaneous value of the squared force due to this bias potentialwallHH: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dHH.* ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1.0 #OFFSET=1.3


The LOWER_WALLS action with label wallHH calculates the following quantities:
 Quantity   
 Description  
wallHH.bias
the instantaneous value of the bias potential
wallHH.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f