PLUMED-NEST

Project ID: plumID:19.061
Source: diffusion_meta.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 the simulation
RESTARTActivate restart. More details

#Define the guest molecule in the simulation
The RESTART action with label  calculates somethingguestThe GROUP action with label guest calculates the following quantities:
 Quantity   
 Type   
 Description  
guest
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=169-186
guest_comThe COM action with label guest_com calculates the following quantities:
 Quantity   
 Type   
 Description  
guest_com
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=guest

#Define the cage centre of mass
centre_comThe COM action with label centre_com calculates the following quantities:
 Quantity   
 Type   
 Description  
centre_com
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=1-168

#Define the centres of the windows as the centre of the three phenyl H atoms in the window
circle1The CENTER_FAST action with label circle1 calculates the following quantities:
 Quantity   
 Type   
 Description  
circle1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=22,78,134
circle2The CENTER_FAST action with label circle2 calculates the following quantities:
 Quantity   
 Type   
 Description  
circle2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=36,64,162
circle3The CENTER_FAST action with label circle3 calculates the following quantities:
 Quantity   
 Type   
 Description  
circle3
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=8,106,148
circle4The CENTER_FAST action with label circle4 calculates the following quantities:
 Quantity   
 Type   
 Description  
circle4
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=50,92,120

#Define distances between the guest centre of mass and the centres of the windows of interest
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=guest_com,circle1
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=guest_com,circle2

#Define distances that will need energetic walls - these are the distances to the other two windows and the overall distance from the cage centre of mass
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=guest_com,circle3
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=guest_com,circle4
dcThe DISTANCE action with label dc calculates the following quantities:
 Quantity   
 Type   
 Description  
dc
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=centre_com,guest_com

lwallsThe LOWER_WALLS action with label lwalls calculates the following quantities:
 Quantity   
 Type   
 Description  
lwalls.bias
scalar
the instantaneous value of the bias potential
lwalls.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3,d4 ATthe positions of the wall=0.25,0.25 KAPPAthe force constant for the wall=4500,4500 OFFSET the offset for the start of the wall=0,0 EXP the powers for the walls=2,2 EPS the values for s_i in the expression for a wall=1,1
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.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=dc ATthe positions of the wall=0.45 KAPPAthe force constant for the wall=3500 OFFSET the offset for the start of the wall=0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1

#Deposit Gaussians, with the distances d1 and d2 as the collective variable
metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d1,d2 SIGMAthe widths of the Gaussian hills=0.01,0.01 HEIGHTthe heights of the Gaussian hills=1.2 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=-2.0,-2.0 GRID_MAXthe upper bounds for the grid=6.0,6.0 GRID_BINthe number of bins for the grid=4000,4000 
meta: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=d1,d2 SIGMAthe widths of the Gaussian hills=0.01,0.01 HEIGHTthe heights of the Gaussian hills=1.2 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=-2.0,-2.0 GRID_MAXthe upper bounds for the grid=6.0,6.0 GRID_BINthe number of bins for the grid=4000,4000  FILE a file in which the list of added hills is stored=HILLS

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,meta.*,uwall.*,lwalls.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=2000