PLUMED-NEST

Project ID: plumID:19.079
Source: nest/tio2_glu/plumed.dat
Originally used with PLUMED version: 2.4.2
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. 

# Ref atom on surf
refThe GROUP action with label ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ref
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=2572

# Entire peptide COM to surface
cThe COM action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
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=1-27
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ref,c COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances

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=mtdThe METAD action with label mtd calculates the following quantities:
 Quantity   
 Type   
 Description  
mtd.bias
scalar
the instantaneous value of the bias potential
ARGthe labels of the scalars on which the bias will act=d.z 
PACEthe frequency for hill addition=1000
BIASFACTORuse well tempered metadynamics and use this bias factor=10
HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=0.01
FILE a file in which the list of added hills is stored=HILLS
GRID_MINthe lower bounds for the grid=-1
GRID_MAXthe upper bounds for the grid=10
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

## wall 
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d.z ATthe positions of the wall=3.0 KAPPAthe force constant for the wall=50000 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=1000 FILEthe name of the file on which to output these quantities=COLVAR