Project ID: plumID:21.023
Source: Data-mb/mb-wtm-bf3/plumed.dat
Originally used with PLUMED version: 2.7
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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=./MuellerBrown-Potential.dat
# INCLUDE FILE=./MuellerBrown-Potential.dat
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
The INCLUDE action with label ./MuellerBrown-Potential.dat calculates somethingUNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label calculates somethingscaling_factorThe CONSTANT action with label scaling_factor calculates the following quantities:| Quantity | Type | Description |
| scaling_factor | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=0.2
pThe DISTANCE action with label p calculates the following quantities:| Quantity | Type | Description |
| p.x | scalar | the x-component of the vector connecting the two atoms |
| p.y | scalar | the y-component of the vector connecting the two atoms |
| p.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=1,2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
CUSTOMCalculate a combination of variables using a custom expression. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=potThe CUSTOM action with label pot calculates the following quantities:| Quantity | Type | Description |
| pot | scalar | an arbitrary function |
ARGthe values input to this function=p.x,p.y,scaling_factor
VARthe names to give each of the arguments in the function=x,y,sf
FUNCthe function you wish to evaluate=sf*(-200*exp(-(x-1)^2-10*y^2)-100*exp(-x^2-10*(y-0.5)^2)-170*exp(-6.5*(x+0.5)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(x+1)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2)+146.699489200588)
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... CUSTOM
bvThe BIASVALUE action with label bv calculates the following quantities:| Quantity | Type | Description |
| bv.bias | scalar | the instantaneous value of the bias potential |
| bv.pot_bias | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named pot |
: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=pot
# --- End of included input ---
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. 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 |
| mtd.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. |
| mtd.rct | scalar | the reweighting factor c(t). |
ARGthe labels of the scalars on which the bias will act=p.x,p.y
PACEthe frequency for hill addition=100
SIGMAthe widths of the Gaussian hills=0.1,0.1
HEIGHTthe heights of the Gaussian hills=1.5
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
BIASFACTORuse well tempered metadynamics and use this bias factor=3
GRID_MINthe lower bounds for the grid=-5,-5
GRID_MAXthe upper bounds for the grid=5,5
GRID_BINthe number of bins for the grid=500,500
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=mtd
ARGthe labels of the scalars on which the bias will act=p.x,p.y
PACEthe frequency for hill addition=100
SIGMAthe widths of the Gaussian hills=0.1,0.1
HEIGHTthe heights of the Gaussian hills=1.5
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
BIASFACTORuse well tempered metadynamics and use this bias factor=3
GRID_MINthe lower bounds for the grid=-5,-5
GRID_MAXthe upper bounds for the grid=5,5
GRID_BINthe number of bins for the grid=500,500
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
FILE a file in which the list of added hills is stored=HILLS
... METAD
wThe REWEIGHT_METAD action with label w calculates the following quantities:| Quantity | Type | Description |
| w | scalar | the weight to use for this frame to negate the effect the metadynamics bias |
: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action has hidden defaults. More details TEMPthe system temperature=1
w: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action uses the defaults shown here. More details TEMPthe system temperature=1 ARG the biases that must be taken into account when reweighting=*.rbias
PRINTPrint quantities to a file. More details 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.data STRIDE the frequency with which the quantities of interest should be output=200
