PLUMED-NEST

Project ID: plumID:22.045
Source: plumed-METAD.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

WHOLEMOLECULESThis 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=1-4053

The WHOLEMOLECULES 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=1912,4012  LABELa label for the action so that its output can be referenced in the input to other actions=d0The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Type   
 Description  
d0
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3966,4009  LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3082,1912  LABELa label for the action so that its output can be referenced in the input to other actions=hiserThe DISTANCE action with label hiser calculates the following quantities:
 Quantity   
 Type   
 Description  
hiser
scalar
the DISTANCE between this pair of atoms

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4013,1912  LABELa label for the action so that its output can be referenced in the input to other actions=deThe DISTANCE action with label de calculates the following quantities:
 Quantity   
 Type   
 Description  
de
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4013,1916  LABELa label for the action so that its output can be referenced in the input to other actions=holeThe DISTANCE action with label hole calculates the following quantities:
 Quantity   
 Type   
 Description  
hole
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4013,842   LABELa label for the action so that its output can be referenced in the input to other actions=hole2The DISTANCE action with label hole2 calculates the following quantities:
 Quantity   
 Type   
 Description  
hole2
scalar
the DISTANCE between this pair of atoms

METADUsed to performed metadynamics on one or more collective variables. More details ...
        ARGthe labels of the scalars on which the bias will act=hole,hole2 PACEthe frequency for hill addition=400 HEIGHTthe heights of the Gaussian hills=0.1 SIGMAthe widths of the Gaussian hills=0.05,0.05 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=30.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 GRID_MINthe lower bounds for the grid=-1,-1 GRID_MAXthe upper bounds for the grid=2,2
 ... METAD

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=hole,hole2 ATthe positions of the wall=0.6,0.6 KAPPAthe force constant for the wall=15000,15000 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1,1 OFFSET the offset for the start of the wall=0,0 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
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=2.3 KAPPAthe force constant for the wall=550  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=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

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=200 FILEthe name of the file on which to output these quantities=COLVAR