PLUMED-NEST

Project ID: plumID:23.015
Source: OPEX_and_METAD/github_metad_0d/plumed.dat
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

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=1-295 ENTITY1the atoms that make up a molecule that you wish to align=296-590

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=1-295
c2The CENTER_FAST action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
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=296-590

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
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=c1,c2

OWThe GROUP action with label OW calculates the following quantities:
 Quantity   
 Type   
 Description  
OW
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=591-40598:3
cn1The COORDINATION action with label cn1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =16 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500
cn1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =16 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
cn2The COORDINATION action with label cn2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =16 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500
cn2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =16 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
cnaThe CUSTOM action with label cna calculates the following quantities:
 Quantity   
 Type   
 Description  
cna
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cn1,cn2 FUNCthe function you wish to evaluate=0.5*(x+y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ...
   ARGthe labels of the scalars on which the bias will act=d,cna
   PACEthe frequency for hill addition=500
   HEIGHTthe heights of the Gaussian hills=3 BIASFACTORuse well tempered metadynamics and use this bias factor=15
   SIGMAthe widths of the Gaussian hills=0.1,2
   FILE a file in which the list of added hills is stored=HILLS
...

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=d ATthe positions of the wall=3.5 KAPPAthe force constant for the wall=10000
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=d ATthe positions of the wall=1.2 KAPPAthe force constant for the wall=10000

PRINTPrint quantities to a file. More details  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.data ARGthe labels of the values that you would like to print to the file=*