PLUMED-NEST

Project ID: plumID:19.077
Source: ASP_NNH.dat
Originally used with PLUMED version: 2.4
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
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=asp.pdb

The MOLINFO action with label  calculates somethingc1The COM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by COM action: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-24 #COM from peptide to surface 
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1916,c1 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 #dist peptide to surface

#restraint 
wall1The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
wall1.bias
scalar
the instantaneous value of the bias potential
wall1.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1.z 
AT
the positions of the wall
=3.0 
KAPPA
the force constant for the wall
=1500

#pb
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=d1.z
SIGMA
the widths of the Gaussian hills
=0.05
HEIGHT
the heights of the Gaussian hills
=0.2 #kj/mol
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
GRID_MIN
the lower bounds for the grid
=0.0
GRID_MAX
the upper bounds for the grid
=7.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
FILE
 a file in which the list of added hills is stored
=HILLS.d1
... METAD


PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.z,metad.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