PLUMED-NEST-TEST-SITE

Project ID: plumID:19.061
Source: ple_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 cage and guest centres of mass and the distance between them
The RESTART action with label  calculates somethingcage_comThe COM action with label cage_com calculates the following quantities:
 Quantity   
 Type   
 Description  
cage_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
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=169-186

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=cage_com,guest_com NOPBC ignore the periodic boundary conditions when calculating distances

#Define the energetic wall for the system, to prevent the guest moving too far from the cage
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=d1 ATthe positions of the wall=2.4 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

#Deposit Gaussians using the distance between the centres of mass as the collective variable, and print the output to the COLVAR file
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 SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 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 GRID_MINthe lower bounds for the grid=-1.0 GRID_MAXthe upper bounds for the grid=5.0 GRID_BINthe number of bins for the grid=2400
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 SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 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 GRID_MINthe lower bounds for the grid=-1.0 GRID_MAXthe upper bounds for the grid=5.0 GRID_BINthe number of bins for the grid=2400  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,meta.*,uwall.* 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