PLUMED-NEST-TEST-SITE

Project ID: plumID:19.063
Source: plumed_path.dat
Originally used with PLUMED version: 2.1
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

#RESTART

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=1-4570 ENTITY1the atoms that make up a molecule that you wish to align=28695-28736

The WHOLEMOLECULES action with label  calculates somethingpThe 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=frameset.pdb  LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=148.2864349416589 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=0.1,0.01 HEIGHTthe heights of the Gaussian hills=0.84 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 BIASFACTORuse well tempered metadynamics and use this bias factor=15 PACEthe frequency for hill addition=500
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=0.1,0.01 HEIGHTthe heights of the Gaussian hills=0.84 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 BIASFACTORuse well tempered metadynamics and use this bias factor=15 PACEthe frequency for hill addition=500  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=0.16 KAPPAthe force constant for the wall=400000.0
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=2  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=81 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,uwall_z.bias,lwall_s_o.bias,uwall_s_i.bias 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