PLUMED-NEST

Project ID: plumID:20.019
Source: Crystal-Energy-Landscapes/plumed.dat
Originally used with PLUMED version: 2.3-mod
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

# Avoid too skewed triclinic box
cellThe CELL action with label cell calculates the following quantities:
 Quantity   
 Type   
 Description  
cell.ax
scalar
the ax component of the cell matrix
cell.ay
scalar
the ay component of the cell matrix
cell.az
scalar
the az component of the cell matrix
cell.bx
scalar
the bx component of the cell matrix
cell.by
scalar
the by component of the cell matrix
cell.bz
scalar
the bz component of the cell matrix
cell.cx
scalar
the cx component of the cell matrix
cell.cy
scalar
the cy component of the cell matrix
cell.cz
scalar
the cz component of the cell matrix: CELLGet the components of the simulation cell More details

bxThe MATHEVAL action with label bx calculates the following quantities:
 Quantity   
 Type   
 Description  
bx
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cell.bx,cell.ax FUNCthe function you wish to evaluate=abs(x)-0.5*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cxThe MATHEVAL action with label cx calculates the following quantities:
 Quantity   
 Type   
 Description  
cx
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cell.cx,cell.ax FUNCthe function you wish to evaluate=abs(x)-0.5*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cyThe MATHEVAL action with label cy calculates the following quantities:
 Quantity   
 Type   
 Description  
cy
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cell.cy,cell.by FUNCthe function you wish to evaluate=abs(x)-0.5*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=bx,cx,cy ATthe positions of the wall=0.0,0.0,0.0 KAPPAthe force constant for the wall=100000.0,100000.0,100000.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1,1,1 OFFSET the offset for the start of the wall=0.3,0.3,0.3 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

# CV1 - Density
volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: VOLUMECalculate the volume the simulation box. More details
densityThe MATHEVAL action with label density calculates the following quantities:
 Quantity   
 Type   
 Description  
density
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=vol FUNCthe function you wish to evaluate=400.0/x*1.66054*118.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Constraints to force the system to stay in the grid 
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=density ATthe positions of the wall=1800 KAPPAthe force constant for the wall=100.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=25 LABELa label for the action so that its output can be referenced in the input to other actions=ulimitThe UPPER_WALLS action with label ulimit calculates the following quantities:
 Quantity   
 Type   
 Description  
ulimit.bias
scalar
the instantaneous value of the bias potential
ulimit.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=density ATthe positions of the wall=1200 KAPPAthe force constant for the wall=100.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=25 LABELa label for the action so that its output can be referenced in the input to other actions=llimitThe LOWER_WALLS action with label llimit calculates the following quantities:
 Quantity   
 Type   
 Description  
llimit.bias
scalar
the instantaneous value of the bias potential
llimit.force2
scalar
the instantaneous value of the squared force due to this bias potential

#CV2 - Potential Energy 
ene_potThe ENERGY action with label ene_pot calculates the following quantities:
 Quantity   
 Type   
 Description  
ene_pot
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details
elattThe MATHEVAL action with label elatt calculates the following quantities:
 Quantity   
 Type   
 Description  
elatt
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=ene_pot,uwall.bias,ulimit.bias,llimit.bias VARthe names to give each of the arguments in the function=a,b,c,d FUNCthe function you wish to evaluate=(a-b-c-d)/400.0+350.507 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# WTmetaD Parameters
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
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
ARGthe labels of the scalars on which the bias will act=elatt,density
PACEthe frequency for hill addition=1000
HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=2.0,20.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
BIASFACTORuse well tempered metadynamics and use this bias factor=200.0
GRID_MINthe lower bounds for the grid=-120,1200
GRID_MAXthe upper bounds for the grid=400,1800
GRID_BINthe number of bins for the grid=5200,600
# PLUMED 2.3 syntax
# REWEIGHTING_NGRID=5200,600
# REWEIGHTING_NHILLS=10
# PLUMED 2.4 syntax
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# RCT_USTRIDE=10
FILE a file in which the list of added hills is stored=HILLS
... METAD

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=elatt,density,metad.bias,metad.rbias,metad.rct,ulimit.bias,llimit.bias,uwall.bias FILEthe name of the file on which to output these quantities=COLVAR