Project ID: plumID:22.034
Source: plumed_meta.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
tested onv2.10
tested onmaster
#
# Avoid too tilted simulation boxes
#

cell: CELLCalculate the components of the simulation cell More details
asb_bx: 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
asb_cx: 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
asb_cy: 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=asb_bx,asb_cx,asb_cy
ATthe positions of the wall=0.0,0.0,0.0
KAPPAthe force constant for the wall=1000000,1000000,1000000
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=0.05,0.05,0.05
LABELa label for the action so that its output can be referenced in the input to other actions=ASB
... UPPER_WALLS

#
# Set limits for non-diagonal elements of the simulation box
#

# Box Angles
# cell: CELL
bx: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cell.bx FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Wall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=bx
ATthe positions of the wall=5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=bx_upper
... UPPER_WALLS

# Wall
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=bx
ATthe positions of the wall=-5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=bx_lower
... LOWER_WALLS

# Box Angles
# cell: CELL
cx: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cell.cx FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Wall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=cx
ATthe positions of the wall=5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=cx_upper
... UPPER_WALLS

# Wall
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=cx
ATthe positions of the wall=-5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=cx_lower
... LOWER_WALLS

# Box Angles
# cell: CELL
cy: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cell.cy FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Wall
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=cy
ATthe positions of the wall=5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=cy_upper
... UPPER_WALLS

# Wall
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=cy
ATthe positions of the wall=-5.75
KAPPAthe force constant for the wall=10000
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=0.0
LABELa label for the action so that its output can be referenced in the input to other actions=cy_lower
... LOWER_WALLS

#
# Metadynamics 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=meta
ARGthe labels of the scalars on which the bias will act=bx,cx,cy
PACEthe frequency for hill addition=1000
HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=0.1,0.1,0.1
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
GRID_MINthe lower bounds for the grid=-6.0,-6.0,-6.0
GRID_MAXthe upper bounds for the grid=6.0,6.0,6.0
GRID_BINthe number of bins for the grid=240,240,240
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
FILE a file in which the list of added hills is stored=HILLS
... METAD

rct_mol: 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=meta.rct FUNCthe function you wish to evaluate=x/252.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # 252 = number of molecules

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=bx,cx,cy,meta.bias,meta.rbias,meta.rct,rct_mol,ASB.bias,bx_lower.bias,bx_upper.bias,cx_lower.bias,cx_upper.bias,cy_lower.bias,cy_upper.bias FILEthe name of the file on which to output these quantities=plumed_meta_COLVAR

# 
# Committor
#

# Stop simulation after energy cutoff is reached
COMMITTORDoes a committor analysis. More details ...
ARGthe labels of the values which is being used to define the committor surface=rct_mol
STRIDE the frequency with which the CVs are analyzed=100000
BASIN_LL1List of lower limits for basin #=4.0
BASIN_UL1List of upper limits for basin #=14.0
... COMMITTOR

# Stop simulation after the DRMSD cutoff is reached
DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut. More details ...
REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=plumed_meta.pdb 
LOWER_CUTOFFonly pairs of atoms further than LOWER_CUTOFF are considered in the calculation=0.1 
UPPER_CUTOFFonly pairs of atoms closer than UPPER_CUTOFF are considered in the calculation=0.8
TYPE what kind of DRMSD would you like to calculate=INTER-DRMSD
LABELa label for the action so that its output can be referenced in the input to other actions=drmsd
... DRMSD

PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=plumed_meta_DRMSD ARGthe labels of the values that you would like to print to the file=drmsd STRIDE the frequency with which the quantities of interest should be output=1000

COMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=drmsd
  STRIDE the frequency with which the CVs are analyzed=100000
  BASIN_LL1List of lower limits for basin #=0.5
  BASIN_UL1List of upper limits for basin #=10.5
... COMMITTOR