PLUMED-NEST-TEST-SITE

Project ID: plumID:24.021
Source: molecular-dynamics/proton-transfer/plumed.dat
Originally used with PLUMED version: 2.8
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

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 

coordThe COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Type   
 Description  
coord
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3,4,5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7-595:3,8-596:3 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.095 D_MAX=0.16}

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=d,coord PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=40 TEMP temperature=330 STRIDEthe frequency with which the forces due to the bias should be calculated=2
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=d,coord PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=40 TEMP temperature=330 STRIDEthe frequency with which the forces due to the bias should be calculated=2  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

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=d ATthe positions of the wall=0.9 KAPPAthe force constant for the wall=2000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=2

uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall2.bias
scalar
the instantaneous value of the bias potential
uwall2.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=coord ATthe positions of the wall=1. KAPPAthe force constant for the wall=2000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=2

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR