PLUMED-NEST-TEST-SITE

Project ID: plumID:20.006
Source: metad_GCGR/plumed.dat
Originally used with PLUMED version: 2.4.3
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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=nowat.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-471 ENTITY1the atoms that make up a molecule that you wish to align=472-6973 STRIDE the frequency with which molecules are reassembled=1

openThe RMSD action with label open calculates the following quantities:
 Quantity   
 Type   
 Description  
open
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.open.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
open: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.open.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
closedThe RMSD action with label closed calculates the following quantities:
 Quantity   
 Type   
 Description  
closed
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.closed.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
closed: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=model.TM.closed.skipped.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

COMBINECalculate a polynomial combination of a set of other variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=progThe COMBINE action with label prog calculates the following quantities:
 Quantity   
 Type   
 Description  
prog
scalar
a linear compbination
  ARGthe values input to this function=open,closed
  COEFFICIENTS the coefficients of the arguments in your function=1,-1
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=distThe COMBINE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
scalar
a linear compbination
  ARGthe values input to this function=open,closed
  COEFFICIENTS the coefficients of the arguments in your function=1,1
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

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=wteThe METAD action with label wte calculates the following quantities:
 Quantity   
 Type   
 Description  
wte.bias
scalar
the instantaneous value of the bias potential
  ARGthe labels of the scalars on which the bias will act=ene
  PACEthe frequency for hill addition=500000000 # 10us
  HEIGHTthe heights of the Gaussian hills=5 SIGMAthe widths of the Gaussian hills=1000
  FILE a file in which the list of added hills is stored=HILLS_WTE.0
  BIASFACTORuse well tempered metadynamics and use this bias factor=20.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
  GRID_MINthe lower bounds for the grid=-1500000 GRID_MAXthe upper bounds for the grid=-500000 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=10
... 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
  ARGthe labels of the scalars on which the bias will act=prog,dist
  SIGMAthe widths of the Gaussian hills=0.05,0.05 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500
  BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
  GRID_MINthe lower bounds for the grid=-1.2,0.5 GRID_MAXthe upper bounds for the grid=1.2,2.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.005
  FILE a file in which the list of added hills is stored=HILLS
... METAD


UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=open,closed,dist ATthe positions of the wall=1.2,1.2,1.6 KAPPAthe force constant for the wall=3000.0,3000.0,3000.0 LABELa label for the action so that its output can be referenced in the input to other actions=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


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 FMTthe format that should be used to output real numbers=%8.4f