PLUMED-NEST

Project ID: plumID:21.034
Source: PBMETA/02/plumed.dat
Originally used with PLUMED version: 2.5
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

dih-000-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1,5,22,24
The TORSION action with label dih-000-01 calculates a scalar quantitydih-001-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=22,24,26,43
The TORSION action with label dih-001-00 calculates a scalar quantitydih-001-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=24,26,43,45
The TORSION action with label dih-001-01 calculates a scalar quantitydih-002-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=43,45,47,55
The TORSION action with label dih-002-00 calculates a scalar quantitydih-002-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=45,47,55,57
The TORSION action with label dih-002-01 calculates a scalar quantitydih-003-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=55,57,61,69
The TORSION action with label dih-003-00 calculates a scalar quantitydih-003-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=57,61,69,71
The TORSION action with label dih-003-01 calculates a scalar quantitydih-004-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=69,71,73,84
The TORSION action with label dih-004-00 calculates a scalar quantitydih-004-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=71,73,84,86
The TORSION action with label dih-004-01 calculates a scalar quantitydih-005-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=84,86,88,98
The TORSION action with label dih-005-00 calculates a scalar quantitydih-005-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=86,88,98,100
The TORSION action with label dih-005-01 calculates a scalar quantitydih-006-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=98,100,102,105
The TORSION action with label dih-006-00 calculates a scalar quantitydih-006-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=100,102,105,107
The TORSION action with label dih-006-01 calculates a scalar quantitydih-007-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=105,107,109,119
The TORSION action with label dih-007-00 calculates a scalar quantitydih-007-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=107,109,119,121
The TORSION action with label dih-007-01 calculates a scalar quantitydih-008-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=119,121,123,143
The TORSION action with label dih-008-00 calculates a scalar quantitydih-008-01: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=121,123,143,145
The TORSION action with label dih-008-01 calculates a scalar quantitydih-009-00: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=143,145,147,164

The TORSION action with label dih-009-00 calculates a scalar quantity
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=dih-000-01,dih-001-00,dih-001-01,dih-002-00,dih-002-01,dih-003-00,dih-003-01,dih-004-00,dih-004-01,dih-005-00,dih-005-01,dih-006-00,dih-006-01,dih-007-00,dih-007-01,dih-008-00,dih-008-01,dih-009-00
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03
SIGMA
the widths of the Gaussian hills
=0.015 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi
GRID_MAX
the upper bounds for the grid
=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
HEIGHT
the height of the Gaussian hills, one for all biases
=0.5 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=10 
PACE
the frequency for hill addition, one for all biases
=500
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=340.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_dih-000-01,HILLS_dih-001-00,HILLS_dih-001-01,HILLS_dih-002-00,HILLS_dih-002-01,HILLS_dih-003-00,HILLS_dih-003-01,HILLS_dih-004-00,HILLS_dih-004-01,HILLS_dih-005-00,HILLS_dih-005-01,HILLS_dih-006-00,HILLS_dih-006-01,HILLS_dih-007-00,HILLS_dih-007-01,HILLS_dih-008-00,HILLS_dih-008-01,HILLS_dih-009-00
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
...

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
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the input for this action is the scalar output from one or more other actions
=dih-000-01,dih-001-00,dih-001-01,dih-002-00,dih-002-01,dih-003-00,dih-003-01,dih-004-00,dih-004-01,dih-005-00,dih-005-01,dih-006-00,dih-006-01,dih-007-00,dih-007-01,dih-008-00,dih-008-01,dih-009-00,pb.bias 
FILE
the name of the file on which to output these quantities
=COLVAR