PLUMED-NEST

Project ID: plumID:19.023
Source: plumed.dat
Originally used with PLUMED version: 2.3
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

WHOLEMOLECULESThis 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=1,5,6,7,9,11,15,16,17,19
#variables
The WHOLEMOLECULES action with label  calculates somethingphiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the 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=1,5,6,7,9,11,15,16,17,19
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=phi,psi,rg 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
#Well-tempered MetaD lines, one for each CV. For each replica the value of the BIASFACTOR should be changed.
aThe METAD action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a.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=phi SIGMAthe widths of the Gaussian hills=0.3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=12 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi FILE a file in which the list of added hills is stored=HILLSphi
bThe METAD action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b.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=psi SIGMAthe widths of the Gaussian hills=0.3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=12 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi FILE a file in which the list of added hills is stored=HILLSpsi
cThe METAD action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c.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=rg SIGMAthe widths of the Gaussian hills=0.007 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=12 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=0.4 FILE a file in which the list of added hills is stored=HILLSrg