PLUMED-NEST

Project ID: plumID:20.031
Source: nanoshuttle_simulations/m16/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

#m16
#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=3343-5951 ENTITY2the atoms that make up a molecule that you wish to align=5952-8560 ENTITY3the atoms that make up a molecule that you wish to align=8561-11169 ENTITY4the atoms that make up a molecule that you wish to align=11170-13778 ENTITY5the atoms that make up a molecule that you wish to align=13779-16387 ENTITY6the atoms that make up a molecule that you wish to align=16388-18996 ENTITY7the atoms that make up a molecule that you wish to align=18997-21605 ENTITY8the atoms that make up a molecule that you wish to align=21606-24214 ENTITY9the atoms that make up a molecule that you wish to align=24215-26823

The WHOLEMOLECULES action with label  calculates somethingc1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2602,2600,2599,2605,2604
The CENTER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the position of the center of massc2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=5296,5298,5299,5301,5306,5295
#d1: DISTANCE ATOMS=c1,c2

The CENTER action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the position of the center of massc3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2604,2605,2606,2608,2612,2610
The CENTER action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.value
the position of the center of massc4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=5306,5301,5302,5303,5304,5305
#d2: DISTANCE ATOMS=c3,c4

The CENTER action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.value
the position of the center of massc5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2602,2600,2599,2605,2604
The CENTER action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.value
the position of the center of massc6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=10849,10851,10852,10854,10859,10848
#d3: DISTANCE ATOMS=c5,c6
#
The CENTER action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.value
the position of the center of massc7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2604,2605,2606,2608,2612,2610
The CENTER action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.value
the position of the center of massc8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=10859,10854,10855,10856,10857,10858
#d1: DISTANCE ATOMS=c7,c8


The CENTER action with label c8 calculates the following quantities:
 Quantity   
 Description  
c8.value
the position of the center of masst1: COORDINATIONCalculate coordination numbers. 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)=5295,5295,5297,5297,5298,5300,5300,5300,5302,10848,10848,10850,10850,10851,10853,10853,10853,10855 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
The COORDINATION action with label t1 calculates the following quantities:
 Quantity   
 Description  
t1.value
the value of the coordinationt3: COORDINATIONCalculate coordination numbers. 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

The COORDINATION action with label t3 calculates the following quantities:
 Quantity   
 Description  
t3.value
the value of the coordinationPBMETADUsed 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=pb 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

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potentialPRINTPrint 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