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

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
=3343-5783 
ENTITY2
the atoms that make up a molecule that you wish to align
=5784-8224 
ENTITY3
the atoms that make up a molecule that you wish to align
=8225-10665 
ENTITY4
the atoms that make up a molecule that you wish to align
=10666-13106 
ENTITY5
the atoms that make up a molecule that you wish to align
=13107-15547 
ENTITY6
the atoms that make up a molecule that you wish to align
=15548-17988 
ENTITY7
the atoms that make up a molecule that you wish to align
=17989-20429 
ENTITY8
the atoms that make up a molecule that you wish to align
=20430-22870 
ENTITY9
the atoms that make up a molecule that you wish to align
=22871-25311

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
=6223,6222,6221,6220,6219,6224
#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
=6216,6214,6213,6224,6219,6217
#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
=14948,14950,14951,14953,14958,14947
#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
=14958,14953,14954,14955,14956,14957
#d1: DISTANCE ATOMS=c7,c8


t1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1182,1183,1183,1182,2654,2654,1588,1527,2056,1182,1183,1183,1182,2654,2654,1588,1527,2056 
GROUPB
Second 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_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
The COORDINATION action with label t1 calculates a scalar quantityt3: 
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

The COORDINATION action with label t3 calculates a scalar quantity
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
The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potential
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