PLUMED-NEST

Project ID: plumID:20.026
Source: plumed_WTMD.dat
Originally used with PLUMED version: 2.5
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

rmsd_a: MULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lis_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
The MULTI_RMSD action with label rmsd_a calculates the following quantities:
 Quantity   
 Description  
rmsd_a.value
the sum of the multiple RMSD distancesrmsd_b: MULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lsd_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
The MULTI_RMSD action with label rmsd_b calculates the following quantities:
 Quantity   
 Description  
rmsd_b.value
the sum of the multiple RMSD distancesMETADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad 
ARGthe labels of the scalars on which the bias will act=rmsd_a,rmsd_b 
SIGMAthe widths of the Gaussian hills=0.01,0.01 
HEIGHTthe heights of the Gaussian hills=1.0 
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 
PACEthe frequency for hill addition=100 
GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=1.1,1.1 
GRID_BINthe number of bins for the grid=400,400
BIASFACTORuse well tempered metadynamics and use this bias factor=5
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=10
FILE a file in which the list of added hills is stored=hills
... METAD
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 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
The PRINT action with label  calculates somethingbias: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=310.15
The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=hist
ARGthe quantities that are being used to construct the histogram=rmsd_a,rmsd_b 
GRID_MIN the lower bounds for the grid=0,0 
GRID_MAX the upper bounds for the grid=1.1,1.1
GRID_BINthe number of bins for the grid=400,400 
BANDWIDTHthe bandwidths for kernel density esimtation=0.05,0.05 
LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
... HISTOGRAM
The HISTOGRAM action with label hist calculates the following quantities:
 Quantity   
 Description  
hist.value
the estimate of the histogram as a function of the argument that was obtainedfes: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hist TEMPthe temperature at which you are operating=310.15
The CONVERT_TO_FES action with label fes calculates the following quantities:
 Quantity   
 Description  
fes.value
the free energy surfaceDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fes FILE the file on which to write the grid=fes STRIDE the frequency with which the grid should be output to the file=1000000