Project ID: plumID:20.031
Source: nanoshuttle_simulations/m04/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
tested onv2.9
tested onmaster
#m04
#RESTART

WHOLEMOLECULES
This 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 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-3342 
ENTITY1
the atoms that make up a molecule that you wish to align
=3343-5699 
ENTITY2
the atoms that make up a molecule that you wish to align
=5700-8056 
ENTITY3
the atoms that make up a molecule that you wish to align
=8057-10413 
ENTITY4
the atoms that make up a molecule that you wish to align
=10414-12770 
ENTITY5
the atoms that make up a molecule that you wish to align
=12771-15127 
ENTITY6
the atoms that make up a molecule that you wish to align
=15128-17484 
ENTITY7
the atoms that make up a molecule that you wish to align
=17485-19841 
ENTITY8
the atoms that make up a molecule that you wish to align
=19842-22198 
ENTITY9
the atoms that make up a molecule that you wish to align
=22199-24555

c1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2602,2600,2599,2605,2604
c2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5128,5127,5138,5133,5131,5130
#d1: DISTANCE ATOMS=c1,c2

c3: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2604,2605,2606,2608,2612,2610
c4: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5133,5138,5137,5136,5135,5134
#d2: DISTANCE ATOMS=c3,c4

c5: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2602,2600,2599,2605,2604
c6: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=22601,22603,22604,22606,22611,22600
#d3: DISTANCE ATOMS=c5,c6
#
c7: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2604,2605,2606,2608,2612,2610
c8: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=22611,22606,22607,22608,22609,22610
#d1: DISTANCE ATOMS=c7,c8


t1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1182,1183,1183,1182,2654,2654,1527,2056,1182,1183,1183,1182,2654,2654,1527,2056 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=5127,5127,5129,5129,5130,5132,5132,5134,22600,22600,22602,22602,22603,22605,22605,22607 
R_0
The 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

t3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=c1,c3,c5,c7  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=c2,c4,c6,c8 
R_0
The 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



PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb 
ARG
the input for this action is the scalar output from one or more other actions
=t1,t3 
SIGMA
the widths of the Gaussian hills
=0.35,0.35 
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 
PACE
the frequency for hill addition, one for all biases
=500 
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_t1,HILLS_t3 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=25 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300

WALKERS_N
number of walkers
=6

WALKERS_ID
walker id
=0

WALKERS_DIR
shared directory with the hills files from all the walkers


WALKERS_RSTRIDE
stride for reading hills files
=500
... PBMETAD

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=t1,t3,pb.bias  
STRIDE
 the frequency with which the quantities of interest should be output
=500   
FILE
the name of the file on which to output these quantities
=COLVAR