PLUMED-NEST

Project ID: plumID:24.010
Source: plumed.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

RESTARTActivate restart. More details
The RESTART 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=1-136
torsion_SSThe TORSION action with label torsion_SS calculates the following quantities:
 Quantity   
 Type   
 Description  
torsion_SS
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,10,91,88
torsion_cycleThe TORSION action with label torsion_cycle calculates the following quantities:
 Quantity   
 Type   
 Description  
torsion_cycle
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,34,68,86

# Metadynamics
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=torsion_SS,torsion_cycle
GRID_MINthe lower bounds for the grid=-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi
SIGMAthe widths of the Gaussian hills=0.3,0.3
HEIGHTthe heights of the Gaussian hills=1.0
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.
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=100
... METAD
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=torsion_SS,torsion_cycle
GRID_MINthe lower bounds for the grid=-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi
SIGMAthe widths of the Gaussian hills=0.3,0.3
HEIGHTthe heights of the Gaussian hills=1.0
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.
LABELa label for the action so that its output can be referenced in the input to other actions=metad
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=100
 FILE a file in which the list of added hills is stored=HILLS
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=torsion_SS,torsion_cycle,metad.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500