PLUMED-NEST-TEST-SITE

Project ID: plumID:23.046
Source: github/Sun/plumed.dat
Originally used with PLUMED version: 2.7.1
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

# This is the plumed file to use on linear native MJ25 - using 2 CVs
#RESTART 

# units 
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

# Molecule
The UNITS action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-226 

# distances 
# first is 1N-8CD and the others are for the CA of resid12 to resids 1to8
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=12,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=32,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=39,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=50,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=80,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=86,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=105,155 	LABELa label for the action so that its output can be referenced in the input to other actions=d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms

CV1The DISTANCE action with label CV1 calculates the following quantities:
 Quantity   
 Type   
 Description  
CV1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,110
CV2The COMBINE action with label CV2 calculates the following quantities:
 Quantity   
 Type   
 Description  
CV2
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ...
	ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8
	COEFFICIENTS the coefficients of the arguments in your function=-0.2552,-0.0358,-0.5991,-0.1338,-0.4747,-0.4192,-0.3914,-0.0502
	PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
...

# activade well-tempered metadynamics
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=CV1,CV2 ...
   # Deposit a Gaussian every 500 time steps (= 1ps), with initial height 
   # equal to 5 kJ/mol and bias factor equal to 10 
   # This version we use a double value for the height and bias factor
   PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=5 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
   # Gaussian width (sigma) should be chosen based on the CV fluctuations in unbiased run 
   # try 1/2 or 1/3 of the estimated fluctuations 
   # standard deviation for distance 1N - 8N was 0.91
   # standard deviation for CA distances was between 6.84-7.06
   SIGMAthe widths of the Gaussian hills=0.5,3.5 
   # Gaussians will be written to file and also stored on grid 
   FILE a file in which the list of added hills is stored=HILLS 
   GRID_WSTRIDEwrite the grid to a file every N steps=100000  
#GRID_RFILE=grid1.dat 
GRID_WFILEthe file on which to write the grid=grid1.dat 
   GRID_NOSPLINE don't use spline interpolation with grids
   GRID_MINthe lower bounds for the grid=0,-100
   GRID_MAXthe upper bounds for the grid=35,0
   GRID_BINthe number of bins for the grid=350,200
...
# Print both collective variables on COLVAR file every 100 steps
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,CV1,CV2,metad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100