PLUMED-NEST

Project ID: plumID:23.035
Source: Y4R_SRS_Gi/MW-WT-MetaD_Y4R-SRS-Gi/plumed.dat
Originally used with PLUMED version: 2.7.3
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

#RESTART
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-10746

The WHOLEMOLECULES action with label  calculates somethingc1The CENTER_FAST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=4088,1562 NOPBC ignore the periodic boundary conditions when calculating distances # center 252TRP-99VAL
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,127 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances # c1 7TYR CA peptide

###FUNNEL_PARAMETERS###
s_centThe CONSTANT action with label s_cent calculates the following quantities:
 Quantity   
 Type   
 Description  
s_cent
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=6.5                                           # INFLEXION
s_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=6.5                                           # INFLEXION  NROWS=0 NCOLS=0
beta_centThe CONSTANT action with label beta_cent calculates the following quantities:
 Quantity   
 Type   
 Description  
beta_cent
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=2.0                                        # STEEPNESS
beta_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=2.0                                        # STEEPNESS  NROWS=0 NCOLS=0
wall_widthThe CONSTANT action with label wall_width calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_width
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.5                                       # WIDTH (h)
wall_width: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.5                                       # WIDTH (h)  NROWS=0 NCOLS=0
wall_bufferThe CONSTANT action with label wall_buffer calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_buffer
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.15                                      # BUFFER (f, total width = WIDTH + BUFFER)
wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.15                                      # BUFFER (f, total width = WIDTH + BUFFER)  NROWS=0 NCOLS=0
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1           # Lower Wall (the starting point of the funnel)
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.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=d1.z ATthe positions of the wall=11.5 KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1           # Upper Wall (the ending point of the funnel)


###########CALCULATE FUNNEL#######
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
        LABELa label for the action so that its output can be referenced in the input to other actions=wall_centerThe MATHEVAL action with label wall_center calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_center
scalar
an arbitrary function
        ARGthe values input to this function=d1.z,s_cent,beta_cent,wall_width,wall_buffer
        VARthe names to give each of the arguments in the function=s,sc,b,h,f
        FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
        PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

########BIAS OF THE WALL######
wall_heightThe CONSTANT action with label wall_height calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_height
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=100.0
wall_height: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe single number that you would like to store=100.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
wall_steepnessThe CONSTANT action with label wall_steepness calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_steepness
scalar
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=500.0
wall_steepness: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUEthe single number that you would like to store=500.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

#######PROYECTION DXY##########
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=dxyThe MATHEVAL action with label dxy calculates the following quantities:
 Quantity   
 Type   
 Description  
dxy
scalar
an arbitrary function
  ARGthe values input to this function=d1.x,d1.y
  VARthe names to give each of the arguments in the function=ax,ay
  FUNCthe function you wish to evaluate=(sqrt(ax*ax+ay*ay))
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

#######DEFINE_POTENTIAL#######
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
        LABELa label for the action so that its output can be referenced in the input to other actions=wall_biasThe MATHEVAL action with label wall_bias calculates the following quantities:
 Quantity   
 Type   
 Description  
wall_bias
scalar
an arbitrary function
        ARGthe values input to this function=dxy,wall_height,wall_steepness,wall_center
        VARthe names to give each of the arguments in the function=z,h,b,zc
        FUNCthe function you wish to evaluate=h*(1.-(1./(1.+exp(b*(z-zc)))))
        PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

finalbiasThe BIASVALUE action with label finalbias calculates the following quantities:
 Quantity   
 Type   
 Description  
finalbias.bias
scalar
the instantaneous value of the bias potential
finalbias.wall_bias_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named wall_bias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias

########DEFINE_METAD###########
METADUsed to performed metadynamics on one or more collective variables. More details ...
        LABELa label for the action so that its output can be referenced in the input to other actions=metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential
meta.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
meta.rct
scalar
the reweighting factor c(t). ARGthe labels of the scalars on which the bias will act=d1.z
        SIGMAthe widths of the Gaussian hills=0.1 HEIGHTthe heights of the Gaussian hills=2
        PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=HILLS
        BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310
        GRID_MINthe lower bounds for the grid=-1 GRID_MAXthe upper bounds for the grid=12 GRID_BINthe number of bins for the grid=300
        CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
	WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

PRINTPrint 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=500 FILEthe name of the file on which to output these quantities=COLVAR