PLUMED-NEST

Project ID: plumID:21.004
Source: HST-GST/CB8-G6/plumed_path.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

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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=1-168 STRIDE the frequency with which molecules are reassembled=1
pThe PATHMSD action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.sss
scalar
the position on the path
p.zzz
scalar
the distance from the path: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=path.pdb  LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=230.0 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 NEIGH_SIZEsize of the neighbor list=8

metaThe METAD action with label meta calculates the following quantities:
 Quantity   
 Type   
 Description  
meta.bias
scalar
the instantaneous value of the bias potential: 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=p.sss,p.zzz SIGMAthe widths of the Gaussian hills=0.2,0.01 HEIGHTthe heights of the Gaussian hills=0.84 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=15 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=1,-0.015 GRID_MAXthe upper bounds for the grid=55,0.19
meta: 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=p.sss,p.zzz SIGMAthe widths of the Gaussian hills=0.2,0.01 HEIGHTthe heights of the Gaussian hills=0.84 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=15 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=1,-0.015 GRID_MAXthe upper bounds for the grid=55,0.19  FILE a file in which the list of added hills is stored=HILLS
uwall_zThe UPPER_WALLS action with label uwall_z calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_z.bias
scalar
the instantaneous value of the bias potential
uwall_z.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.zzz ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=40000000.0
lwall_s_oThe LOWER_WALLS action with label lwall_s_o calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_s_o.bias
scalar
the instantaneous value of the bias potential
lwall_s_o.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.sss ATthe positions of the wall=1  KAPPAthe force constant for the wall=20000.0
uwall_s_iThe UPPER_WALLS action with label uwall_s_i calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_s_i.bias
scalar
the instantaneous value of the bias potential
uwall_s_i.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.sss ATthe positions of the wall=55 KAPPAthe force constant for the wall=20000.0

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p.sss,p.zzz STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLV_Path FMTthe format that should be used to output real numbers=%8.4f