PLUMED-NEST

Project ID: plumID:21.024
Source: aladip/FES_03to96_wat/plumed.dat
Originally used with PLUMED version: 2.4
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

# set up two variables for Phi and Psi dihedral angles
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-22

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 one or multiple torsional angles. 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 one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17

pmThe PROPERTYMAP action with label pm calculates the following quantities:
 Quantity   
 Type   
 Description  
pm.X
scalar
the projection of the instanenous position in CV space on the coordinate X that is defined in the reference file
pm.zzz
scalar
the projection of the instanenous position in CV space on the coordinate zzz that is defined in the reference file: PROPERTYMAPCalculate generic property maps. More details REFERENCEthe pdb is needed to provide the various milestones=reference.pdb PROPERTYthe property to be used in the indexing: this goes in the REMARK field of the reference=X LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=1000
bvXThe BIASVALUE action with label bvX calculates the following quantities:
 Quantity   
 Type   
 Description  
bvX.bias
scalar
the instantaneous value of the bias potential
bvX.pm.X_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named pm.X: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=pm.X

METADUsed to performed metadynamics on one or more collective variables. More details ...
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
ARGthe labels of the scalars on which the bias will act=phi,psi
PACEthe frequency for hill addition=500 
HEIGHTthe heights of the Gaussian hills=1.2 
SIGMAthe widths of the Gaussian hills=0.35,0.35 
FILE a file in which the list of added hills is stored=HILLS 
BIASFACTORuse well tempered metadynamics and use this bias factor=6.0
GRID_MINthe lower bounds for the grid=-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi 
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
... METAD

# monitor the two variables and the metadynamics bias potential
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=phi,psi,pm.X,metad.bias,bvX.pm.X_bias FILEthe name of the file on which to output these quantities=COLVAR