PLUMED-NEST

Project ID: plumID:20.031
Source: nanoshuttle_simulations/m08/plumed.dat
Originally used with PLUMED version: 2.7
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

#m08
#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=1-3342 ENTITY1the atoms that make up a molecule that you wish to align=3343-5783 ENTITY2the atoms that make up a molecule that you wish to align=5784-8224 ENTITY3the atoms that make up a molecule that you wish to align=8225-10665 ENTITY4the atoms that make up a molecule that you wish to align=10666-13106 ENTITY5the atoms that make up a molecule that you wish to align=13107-15547 ENTITY6the atoms that make up a molecule that you wish to align=15548-17988 ENTITY7the atoms that make up a molecule that you wish to align=17989-20429 ENTITY8the atoms that make up a molecule that you wish to align=20430-22870 ENTITY9the atoms that make up a molecule that you wish to align=22871-25311

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=2602,2600,2599,2605,2604
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=6223,6222,6221,6220,6219,6224
#d1: DISTANCE ATOMS=c1,c2

c3The CENTER_FAST action with label c3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c3
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=2604,2605,2606,2608,2612,2610
c4The CENTER_FAST action with label c4 calculates the following quantities:
 Quantity   
 Type   
 Description  
c4
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=6216,6214,6213,6224,6219,6217
#d2: DISTANCE ATOMS=c3,c4

c5The CENTER_FAST action with label c5 calculates the following quantities:
 Quantity   
 Type   
 Description  
c5
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=2602,2600,2599,2605,2604
c6The CENTER_FAST action with label c6 calculates the following quantities:
 Quantity   
 Type   
 Description  
c6
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=14948,14950,14951,14953,14958,14947
#d3: DISTANCE ATOMS=c5,c6
#
c7The CENTER_FAST action with label c7 calculates the following quantities:
 Quantity   
 Type   
 Description  
c7
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=2604,2605,2606,2608,2612,2610
c8The CENTER_FAST action with label c8 calculates the following quantities:
 Quantity   
 Type   
 Description  
c8
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=14958,14953,14954,14955,14956,14957
#d1: DISTANCE ATOMS=c7,c8


t1The COORDINATION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1182,1183,1183,1182,2654,2654,1588,1527,2056,1182,1183,1183,1182,2654,2654,1588,1527,2056 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6213,6213,6215,6215,6216,6218,6218,6218,6220,14947,14947,14949,14949,14950,14952,14952,14952,14954 R_0The r_0 parameter of the switching function=0.50 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
t1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1182,1183,1183,1182,2654,2654,1588,1527,2056,1182,1183,1183,1182,2654,2654,1588,1527,2056 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6213,6213,6215,6215,6216,6218,6218,6218,6220,14947,14947,14949,14949,14950,14952,14952,14952,14954 R_0The r_0 parameter of the switching function=0.50 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
t3The COORDINATION action with label t3 calculates the following quantities:
 Quantity   
 Type   
 Description  
t3
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c1,c3,c5,c7  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=c2,c4,c6,c8 R_0The r_0 parameter of the switching function=0.60 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
t3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c1,c3,c5,c7  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=c2,c4,c6,c8 R_0The r_0 parameter of the switching function=0.60 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0

PBMETADUsed to performed Parallel Bias metadynamics. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=pbThe PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Type   
 Description  
pb.bias
scalar
the instantaneous value of the bias potential ARGthe labels of the scalars on which the bias will act=t1,t3 SIGMAthe widths of the Gaussian hills=0.35,0.35 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 PACEthe frequency for hill addition, one for all biases=500 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_t1,HILLS_t3 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=25 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
WALKERS_Nnumber of walkers=6
WALKERS_IDwalker id=0
WALKERS_DIRshared directory with the hills files from all the walkers=../
WALKERS_RSTRIDEstride for reading hills files=500
... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t3,pb.bias  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