PLUMED-NEST

Project ID: plumID:20.028
Source: wild-type/plumed-1.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

RESTARTActivate restart. More details

The RESTART action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=step5_charmm2gmx-modified-1.pdb
first: 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=3006-3053       #  GTP
The CENTER action with label first calculates the following quantities:
 Quantity   
 Description  
first.value
the position of the center of masssecond: 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=2955-3005      #  FAR
The CENTER action with label second calculates the following quantities:
 Quantity   
 Description  
second.value
the position of the center of masslast: 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=9733-33193:138   #  all P atoms in system--range with a stride 118
The CENTER action with label last calculates the following quantities:
 Quantity   
 Description  
last.value
the position of the center of massgtp: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=first,last COMPONENTS calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label gtp calculates the following quantities:
 Quantity   
 Description  
gtp.x
the x-component of the vector connecting the two atoms
gtp.y
the y-component of the vector connecting the two atoms
gtp.z
the z-component of the vector connecting the two atoms
gtp.value
the DISTANCE between this pair of atomsfar: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=second,last COMPONENTS calculate the x, y and z components of the distance separately and store them as label

# Activate metadynamics in phi and psi
# depositing a Gaussian every 500 time steps,
# with height equal to 1.2 kJoule/mol,
# and width 0.35 rad for both CVs. 

The DISTANCE action with label far calculates the following quantities:
 Quantity   
 Description  
far.x
the x-component of the vector connecting the two atoms
far.y
the y-component of the vector connecting the two atoms
far.z
the z-component of the vector connecting the two atoms
far.value
the DISTANCE between this pair of atomsMETADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad
ARGthe labels of the scalars on which the bias will act=gtp.z,far.z
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.2
SIGMAthe widths of the Gaussian hills=0.10,0.35
FILE a file in which the list of added hills is stored=HILLS2
BIASFACTORuse well tempered metadynamics and use this bias factor=5.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.0
GRID_MINthe lower bounds for the grid=-15.0,-10.0
GRID_MAXthe upper bounds for the grid=15.0,10.0
... METAD

# monitor the two variables and the metadynamics bias potential
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=gtp.z,far.z,metad.bias FILEthe name of the file on which to output these quantities=COLVAR2