Project ID: plumID:23.022
Source: input_data/timelagged/opes-y/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
eneThe CUSTOM action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | 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=0.15*(146.7-280*exp(-15*(x-1)^2+0*(x-1)*(y-0)-10*(y-0)^2)-170*exp(-1*(x-0.2)^2+0*(x-0)*(y-0.5)-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))
potThe BIASVALUE action with label pot calculates the following quantities:| Quantity | Type | Description |
| pot.bias | scalar | the instantaneous value of the bias potential |
| pot.ene_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 ene |
: 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=ene
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.y BARRIERthe free energy barrier to be overcome=15 PACEthe frequency for kernel deposition=200
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.y BARRIERthe free energy barrier to be overcome=15 PACEthe frequency for kernel deposition=200 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 FILE a file in which the list of all deposited kernels is stored=KERNELS
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.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=p.x KAPPAthe force constant for the wall=1000 ATthe positions of the wall=-1.3
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 |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.x KAPPAthe force constant for the wall=1000 ATthe positions of the wall=+1.2
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 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
