PLUMED-NEST

Project ID: plumID:20.002
Source: plumed-MetaD.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

# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
RESTARTActivate restart. More details
The RESTART action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=npt.pdb
proteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-6518
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=protein
p1The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.sss
scalar
the position on the path
p1.zzz
scalar
the distance from the path: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=frameset_CA.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=193.6

#metad: METAD ARG=p1.sss SIGMA=500 SIGMA_MIN=0.005 SIGMA_MAX=0.05 HEIGHT=4.184 ADAPTIVE=DIFF TEMP=300.0 BIASFACTOR=10 PACE=100
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.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=p1.sss,p1.zzz SIGMAthe widths of the Gaussian hills=0.2,0.02 HEIGHTthe heights of the Gaussian hills=0.4184 GRID_SPARSE use a sparse grid to store hills GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=40,18 GRID_BINthe number of bins for the grid=200,200 FILE a file in which the list of added hills is stored=HILLS PACEthe frequency for hill addition=500 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 BIASFACTORuse well tempered metadynamics and use this bias factor=8
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.zzz ATthe positions of the wall=0.16 KAPPAthe force constant for the wall=100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=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

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=colvar_metaD