PLUMED-NEST

Project ID: plumID:19.047
Source: trpcage/close/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

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=1-304
The WHOLEMOLECULES action with label  calculates somethingp1The PROPERTYMAP action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.X
scalar
the projection of the instanenous position in CV space on the coordinate X that is defined in the reference file
p1.Y
scalar
the projection of the instanenous position in CV space on the coordinate Y that is defined in the reference file
p1.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=reframe.pdb PROPERTYthe property to be used in the indexing: this goes in the REMARK field of the reference=X,Y LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=50.0 NEIGH_SIZEsize of the neighbor list=50 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=50 EPSILON the maximum distance between the close and the current structure, the positive value turn on the close structure method=0.01
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=p1.X,p1.Y SIGMAthe widths of the Gaussian hills=0.1,0.1 HEIGHTthe heights of the Gaussian hills=0.5 PACEthe frequency for hill addition=1000 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 LABELa label for the action so that its output can be referenced in the input to other actions=restraintThe METAD action with label restraint calculates the following quantities:
 Quantity   
 Type   
 Description  
restraint.bias
scalar
the instantaneous value of the bias potential
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=p1.X,p1.Y SIGMAthe widths of the Gaussian hills=0.1,0.1 HEIGHTthe heights of the Gaussian hills=0.5 PACEthe frequency for hill addition=1000 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 LABELa label for the action so that its output can be referenced in the input to other actions=restraint  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=p1.X,p1.Y,p1.zzz,restraint.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f