PLUMED-NEST

Project ID: plumID:21.049
Source: 2ad_inter/plumed.3.dat
Originally used with PLUMED version: 2.6
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=../PathCV.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=ps ENERGYthe units of energy=kcal/mol

phi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomswphi: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=phi COEFFICIENTS the coefficients of the arguments in your function=1. PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label wphi calculates the following quantities:
 Quantity   
 Description  
wphi.value
a linear compbinationLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=wphi ATthe positions of the wall=-2.7 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=philwall
The LOWER_WALLS action with label philwall calculates the following quantities:
 Quantity   
 Description  
philwall.bias
the instantaneous value of the bias potential
philwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=wphi ATthe positions of the wall=2.7  KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=phiuwall

The UPPER_WALLS action with label phiuwall calculates the following quantities:
 Quantity   
 Description  
phiuwall.bias
the instantaneous value of the bias potential
phiuwall.force2
the instantaneous value of the squared force due to this bias potentialpsi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomswpsi: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=psi COEFFICIENTS the coefficients of the arguments in your function=1. PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label wpsi calculates the following quantities:
 Quantity   
 Description  
wpsi.value
a linear compbinationLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=wpsi ATthe positions of the wall=-2.7 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=psilwall
The LOWER_WALLS action with label psilwall calculates the following quantities:
 Quantity   
 Description  
psilwall.bias
the instantaneous value of the bias potential
psilwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=wpsi ATthe positions of the wall=2.7  KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=psiuwall

The UPPER_WALLS action with label psiuwall calculates the following quantities:
 Quantity   
 Description  
psiuwall.bias
the instantaneous value of the bias potential
psiuwall.force2
the instantaneous value of the squared force due to this bias potentialPATHCVThis action is not part of PLUMED and was included by using a LOAD command More details LABEL=pcv ARG=phi,psi GENPATH=20,20,20,-1.4,1.2,1.1,-0.8 FIXED=21,40 HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=3 WALKERS_N=4 WALKERS_DIR=. OUTFILE=1_PATH

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pcv.z ATthe positions of the wall=0.0  KAPPAthe force constant for the wall=70.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=tube
The UPPER_WALLS action with label tube calculates the following quantities:
 Quantity   
 Description  
tube.bias
the instantaneous value of the bias potential
tube.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pcv.s ATthe positions of the wall=-0.4 KAPPAthe force constant for the wall=50.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pcv.s ATthe positions of the wall=1.4  KAPPAthe force constant for the wall=50.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall


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 potentialPATHCVThis action is not part of PLUMED and was included by using a LOAD command More details LABEL=pcv0 ARG=phi,psi INFILE=in0_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=0_PATH
PATHCVThis action is not part of PLUMED and was included by using a LOAD command More details LABEL=pcv1 ARG=phi,psi INFILE=in1_path.input FIXED=21,40 HALFLIFE=-1 PACE=0 OUTFILE=1_PATH
s: CUSTOMCalculate a combination of variables using a custom expression. More details NUMERICAL_DERIVATIVES ARGthe values input to this function=pcv0.s,pcv0.z,pcv1.s,pcv1.z VARthe names to give each of the arguments in the function=s0,z0,s1,z1 FUNCthe function you wish to evaluate=((1/z0)/(1/z0+1/z1))*s0+((1/z1)/(1/z0+1/z1))*s1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label s calculates the following quantities:
 Quantity   
 Description  
s.value
an arbitrary functionaux: PATHCVThis action is not part of PLUMED and was included by using a LOAD command More details ARG=phi,psi GENPATH=0,10,0,-1.0,-0.6,0.7,1.0 OUTFILE=AUX
z: CUSTOMCalculate a combination of variables using a custom expression. More details NUMERICAL_DERIVATIVES ARGthe values input to this function=aux.s VARthe names to give each of the arguments in the function=z FUNCthe function you wish to evaluate=z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label z calculates the following quantities:
 Quantity   
 Description  
z.value
an arbitrary functionMOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=steer
 ARGthe labels of the scalars on which the bias will act=pcv.s
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=00000    AT0ATx is equal to the position of the restraint at time STEPx=1.0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1500.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=10000    AT1ATx is equal to the position of the restraint at time STEPx=0.5
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label steer calculates the following quantities:
 Quantity   
 Description  
steer.bias
the instantaneous value of the bias potential
steer.work
the total work performed changing this restraint
steer.force2
the instantaneous value of the squared force due to this bias potential
steer._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
steer._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
steer._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input fileMOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=repel
 ARGthe labels of the scalars on which the bias will act=z
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=00000    AT0ATx is equal to the position of the restraint at time STEPx=0.5 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1500.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=10000    AT1ATx is equal to the position of the restraint at time STEPx=0.5
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label repel calculates the following quantities:
 Quantity   
 Description  
repel.bias
the instantaneous value of the bias potential
repel.work
the total work performed changing this restraint
repel.force2
the instantaneous value of the squared force due to this bias potential
repel._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
repel._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
repel._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=phi,psi,pcv.s,pcv.z,steer.bias,tube.bias,repel.bias,philwall.bias,phiuwall.bias,psilwall.bias,psiuwall.bias,lwall.bias,uwall.bias FILEthe name of the file on which to output these quantities=./1_COLVAR