PLUMED-NEST

Project ID: plumID:20.028
Source: oncogenic/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

RESTART
Activate restart. More details

FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=step5_charmm2gmx-modified-1.pdb
first: 
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
=2964-3014         #FAR
second: 
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
=3015-3062        #GTP
last: 
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
=9742-33202:138     #all P atoms in system--range with a stride 118

far: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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
        #distance between FAR and center of membrane
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 atomsgtp: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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
        #distance between GTP and center of membrane

# depositing a Gaussian every 500 time steps,
# with height equal to 1.0 kJoule/mol,
# and width 0.35 rad for both CVs. 

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
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=gtp.z,far.z
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.10,0.35
FILE
 a file in which the list of added hills is stored
=HILLS1
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.0
GRID_MIN
the lower bounds for the grid
=-16.0,-16.0
GRID_MAX
the upper bounds for the grid
=16.0,16.0
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.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
=200 
ARG
the input for this action is the scalar output from one or more other actions
=gtp.z,far.z,metad.bias 
FILE
the name of the file on which to output these quantities
=COLVAR1