PLUMED-NEST

Project ID: plumID:21.031
Source: plumed.dat
Originally used with PLUMED version: 2.6
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps 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=1-25214
nbd1The COM action with label nbd1 calculates the following quantities:
 Quantity   
 Type   
 Description  
nbd1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=10888-11839,12285-14568 
nbd2The COM action with label nbd2 calculates the following quantities:
 Quantity   
 Type   
 Description  
nbd2
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=21322-24882 
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
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=nbd1,nbd2 NOPBC ignore the periodic boundary conditions when calculating distances

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=60.0 KAPPAthe force constant for the wall=300.0 EXP the powers for the walls=2.0 EPS the values for s_i in the expression for a wall=1.0 OFFSET the offset for the start of the wall=0
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=25.0 KAPPAthe force constant for the wall=300.0 EXP the powers for the walls=2.0 EPS the values for s_i in the expression for a wall=1.0 OFFSET the offset for the start of the wall=0
METADUsed to performed metadynamics on one or more collective variables. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
   ARGthe labels of the scalars on which the bias will act=d PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.0 SIGMAthe widths of the Gaussian hills=0.5 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=20.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.0
   GRID_MINthe lower bounds for the grid=24.0 GRID_MAXthe upper bounds for the grid=61.0 GRID_BINthe number of bins for the grid=150
... METAD
# monitor the variable and the metadynamics bias potential
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=d,metad.bias FILEthe name of the file on which to output these quantities=COLVAR