PLUMED-NEST

Project ID: plumID:21.020
Source: sn2/smd/plumed.inp
Originally used with PLUMED version: 2.8
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

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=1,2 LABELa label for the action so that its output can be referenced in the input to other actions=d1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6 LABELa label for the action so that its output can be referenced in the input to other actions=d2

The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2 COEFFICIENTS the coefficients of the arguments in your function=0.707,-0.707 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=cv

The COMBINE action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.value
a linear compbinationUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2 ATthe positions of the wall=5.0,5.0 KAPPAthe force constant for the wall=100.0,100.0 LABELa label for the action so that its output can be referenced in the input to other actions=constrain

The UPPER_WALLS action with label constrain calculates the following quantities:
 Quantity   
 Description  
constrain.bias
the instantaneous value of the bias potential
constrain.force2
the instantaneous value of the squared force due to this bias potentialMOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=cv
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0     AT0ATx is equal to the position of the restraint at time STEPx=-1.5  KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1000.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=20000 AT1ATx is equal to the position of the restraint at time STEPx=1.5   KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=1000.0
  LABELa label for the action so that its output can be referenced in the input to other actions=res
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
res.work
the total work performed changing this restraint
res.force2
the instantaneous value of the squared force due to this bias potential
res._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
res._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
res._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input fileFLUSHThis 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=2000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv,res.work STRIDE the frequency with which the quantities of interest should be output=2 FILEthe name of the file on which to output these quantities=colvar