PLUMED-NEST

Project ID: plumID:19.078
Source: meta_reweigthing/LJ-38/plumed.dat
Originally used with PLUMED version: 2.5-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

# plumed input file
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label  calculates somethingnsa: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-38 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.25 D_MAX=1.5} 

The COORDINATIONNUMBER action with label nsa calculates the following quantities:
 Quantity   
 Description  
nsa.value
the coordination numbers of the specified atomsns: 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=nsa FUNCthe function you wish to evaluate=exp(-(x-6)*(x-6)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label ns calculates the following quantities:
 Quantity   
 Description  
ns.value
an arbitrary functionne: 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=nsa FUNCthe function you wish to evaluate=exp(-(x-8)*(x-8)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label ne calculates the following quantities:
 Quantity   
 Description  
ne.value
an arbitrary functionmt: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=ns,ne 
PACEthe frequency for hill addition=500 
SIGMAthe widths of the Gaussian hills=0.5,0.5 
BIASFACTORuse well tempered metadynamics and use this bias factor=4 HEIGHTthe heights of the Gaussian hills=0.2 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.168 
GRID_MINthe lower bounds for the grid=0.,0. GRID_MAXthe upper bounds for the grid=25,20 GRID_BINthe number of bins for the grid=300,300
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
mt.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mt.rct
the reweighting factor c(t)PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ns,ne,mt.bias,mt.rct,mt.rbias FMTthe format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500