PLUMED-NEST

Project ID: plumID:19.077
Source: 12mer_NH.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
MOLINFOThis 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 STRUCTUREa file in pdb format containing a reference structure=12mer.pdb

#PEPTIDE DISTANCE#
The MOLINFO action with label  calculates somethingpep1The COM action with label pep1 calculates the following quantities:
 Quantity   
 Type   
 Description  
pep1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-197
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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2473,pep1 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

##radius of gyration##
GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5,29,51,72,84,96,108,120,127,144,161,175 LABELa label for the action so that its output can be referenced in the input to other actions=rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration

##ENERGY##
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=6.0 KAPPAthe force constant for the wall=1500

METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=ene
PACEthe frequency for hill addition=5000 BIASFACTORuse well tempered metadynamics and use this bias factor=25.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=300
GRID_MINthe lower bounds for the grid=-5350000.000000
GRID_MAXthe upper bounds for the grid=-5250000.000000
FILE a file in which the list of added hills is stored=HILLS
... METAD

METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.z,rg
PACEthe frequency for hill addition=250 BIASFACTORuse well tempered metadynamics and use this bias factor=25.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=0.01,0.02
GRID_MINthe lower bounds for the grid=0.0,0.0
GRID_MAXthe upper bounds for the grid=20.0,10.0
FILE a file in which the list of added hills is stored=HILLS_MTD
LABELa label for the action so that its output can be referenced in the input to other actions=cvbiasThe METAD action with label cvbias calculates the following quantities:
 Quantity   
 Type   
 Description  
cvbias.bias
scalar
the instantaneous value of the bias potential
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ene STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR