PLUMED-NEST-TEST-SITE

Project ID: plumID:24.004
Source: glycine/plumed.start.dat
Originally used with PLUMED version: 2.8.1
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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=GraphMol.cpp

# Define groups for the CV
The LOAD action with label  calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=coms_120.dat
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=centers_120.dat
C: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3-1200:10
The GROUP action with label C calculates somethingCA: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2-1200:10
The GROUP action with label CA calculates somethingN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1200:10
 
# Define the CV
The GROUP action with label N calculates somethingGRAPHMOLThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=model
 CENTER=COM
 START1=C
 END1=CA
 START2=N
 END2=C
 START3=N
 END3=CA
 START4=CHcenter
 END4=CA
 KCUT=6
 MODEL=model.pt
... GRAPHMOL

METADUsed 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=model.node-0,model.node-1
 SIGMAthe widths of the Gaussian hills=0.15,0.1 
 HEIGHTthe heights of the Gaussian hills=8.3 # this is 2kt at 500 K 
 FILE a file in which the list of added hills is stored=HILLS   # File where the information of the gaussians is printed
 BIASFACTORuse well tempered metadynamics and use this bias factor=100
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=500.0 
 PACEthe frequency for hill addition=500
 GRID_MINthe lower bounds for the grid=0.0,0.0 GRID_MAXthe upper bounds for the grid=12.0,15.0
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... 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 ARGthe labels of the values that you would like to print to the file=model.*,metad.* 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