PLUMED-NEST

Project ID: plumID:19.064
Source: LKA14/plumed_Amph.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=conf.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=1-287
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2039,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=5,24,46,68,87,106,128,147,166,188,210,229,248,270 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


##Blocks##
B1The COM action with label B1 calculates the following quantities:
 Quantity   
 Type   
 Description  
B1
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=1-84
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2.x
scalar
the x-component of the vector connecting the two atoms
d2.y
scalar
the y-component of the vector connecting the two atoms
d2.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2039,B1 COMPONENTS calculate the x, y and z components of the distance separately and store them as label 
B2The COM action with label B2 calculates the following quantities:
 Quantity   
 Type   
 Description  
B2
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=85-210
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3.x
scalar
the x-component of the vector connecting the two atoms
d3.y
scalar
the y-component of the vector connecting the two atoms
d3.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2039,B2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label 
B3The COM action with label B3 calculates the following quantities:
 Quantity   
 Type   
 Description  
B3
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=211-287
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4.x
scalar
the x-component of the vector connecting the two atoms
d4.y
scalar
the y-component of the vector connecting the two atoms
d4.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2039,B3 COMPONENTS calculate the x, y and z components of the distance separately and store them as label 


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=2500 BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=375
GRID_MINthe lower bounds for the grid=2700000.00000
GRID_MAXthe upper bounds for the grid=3100000.00000
FILE a file in which the list of added hills is stored=HILLS
... METAD

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,d2.z,d3.z,d4.z ATthe positions of the wall=8.0,8.0,8.0,8.0 KAPPAthe force constant for the wall=1500,1500,1500,1500 

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=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 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=-5.0,0.0
GRID_MAXthe upper bounds for the grid=15.0,20.0
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=d1.z,rg,ene,cvbias.bias 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