PLUMED-NEST-TEST-SITE

Project ID: plumID:21.026
Source: plumed_input/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

UNITSThis command sets the internal units for the code. More details  LENGTHthe units of lengths=A  ENERGYthe units of energy=kcal/mol
The UNITS 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=1-5946

distThe DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1614,5843
dist2The DISTANCE action with label dist2 calculates the following quantities:
 Quantity   
 Type   
 Description  
dist2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2838,3207
dist3The DISTANCE action with label dist3 calculates the following quantities:
 Quantity   
 Type   
 Description  
dist3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=473,5093
dist4The DISTANCE action with label dist4 calculates the following quantities:
 Quantity   
 Type   
 Description  
dist4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=473,5843
#between Lys(N+)374 and com of ASP21 ASP65
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=351,1038  LABELa label for the action so that its output can be referenced in the input to other actions=cooThe COM action with label coo calculates the following quantities:
 Quantity   
 Type   
 Description  
coo
atoms
virtual atom calculated by COM action
dist5The DISTANCE action with label dist5 calculates the following quantities:
 Quantity   
 Type   
 Description  
dist5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5767,coo

path1The PATHMSD action with label path1 calculates the following quantities:
 Quantity   
 Type   
 Description  
path1.sss
scalar
the position on the path
path1.zzz
scalar
the distance from the path: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=reference_path-renumb.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=1.46 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=100 NEIGH_SIZEsize of the neighbor list=20


METADUsed to performed metadynamics on one or more collective variables. More details ...
	ARGthe labels of the scalars on which the bias will act=path1.sss,path1.zzz PACEthe frequency for hill addition=400 HEIGHTthe heights of the Gaussian hills=0.1 SIGMAthe widths of the Gaussian hills=1,0.15 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=50.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 GRID_MINthe lower bounds for the grid=-10,-5 GRID_MAXthe upper bounds for the grid=100,15 
... METAD



UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=path1.zzz ATthe positions of the wall=9.0 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 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 STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR