PLUMED-NEST

Project ID: plumID:19.047
Source: cyclo/close/plumed_v2.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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-24
The WHOLEMOLECULES action with label  calculates somethingp1The PROPERTYMAP action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.S1
scalar
the projection of the instanenous position in CV space on the coordinate S1 that is defined in the reference file
p1.S2
scalar
the projection of the instanenous position in CV space on the coordinate S2 that is defined in the reference file
p1.S3
scalar
the projection of the instanenous position in CV space on the coordinate S3 that is defined in the reference file
p1.zzz
scalar
the projection of the instanenous position in CV space on the coordinate zzz that is defined in the reference file: 
PROPERTYMAP
Calculate generic property maps. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=reference.pdb 
PROPERTY
the property to be used in the indexing: this goes in the REMARK field of the reference
=S1,S2,S3 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=300.0 
EPSILON
 the maximum distance between the close and the current structure, the positive value turn on the close structure method
=0.005 
LOG_CLOSE
 value 1 enables logging regarding the close structure
=1
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 
ARG
the labels of the scalars on which the bias will act
=p1.S1,p1.S2,p1.S3 
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02 
HEIGHT
the heights of the Gaussian hills
=0.2 
PACE
the frequency for hill addition
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraintThe METAD action with label restraint calculates the following quantities:
 Quantity   
 Type   
 Description  
restraint.bias
scalar
the instantaneous value of the bias potential
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 
ARG
the labels of the scalars on which the bias will act
=p1.S1,p1.S2,p1.S3 
SIGMA
the widths of the Gaussian hills
=0.02,0.02,0.02 
HEIGHT
the heights of the Gaussian hills
=0.2 
PACE
the frequency for hill addition
=1000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint  
FILE
 a file in which the list of added hills is stored
=HILLS
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=p1.S1,p1.S2,p1.S3,p1.zzz,restraint.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f