Project ID: plumID:24.029
Source: Wolfe-Quapp/opes/plumed.dat
Originally used with PLUMED version: 2.9
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.
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label calculates somethingpThe POSITION action with label p calculates the following quantities:| Quantity | Type | Description |
| p.x | scalar | the x-component of the atom position |
| p.y | scalar | the y-component of the atom position |
| p.z | scalar | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1
doubleWellThe CUSTOM action with label doubleWell calculates the following quantities:| Quantity | Type | Description |
| doubleWell | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ...
FUNCthe function you wish to evaluate=2*(x^4+y^4-2*x^2-4*y^2+2*x*y+0.8*x+0.1*y+9.28)
...
potentialThe BIASVALUE action with label potential calculates the following quantities:| Quantity | Type | Description |
| potential.bias | scalar | the instantaneous value of the bias potential |
| potential.doubleWell_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 doubleWell |
: 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=doubleWell
opesThe OPES_METAD action with label opes calculates the following quantities:| Quantity | Type | Description |
| opes.bias | scalar | the instantaneous value of the bias potential |
| opes.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes.neff | scalar | effective sample size |
| opes.nker | scalar | total number of compressed kernels used to represent the bias |
: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=p.x
PACEthe frequency for kernel deposition=100
BARRIERthe free energy barrier to be overcome=20
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=5000
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=p.x
PACEthe frequency for kernel deposition=100
BARRIERthe free energy barrier to be overcome=20
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=5000
TEMP temperature=-1 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...
PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=p.x,p.y,opes.bias
ENDPLUMEDTerminate plumed input. More details
