PLUMED-NEST

Project ID: plumID:19.020
Source: step-2/plumed.5.dat
Originally used with PLUMED version: 2.2
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

#RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=reference.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-427

a: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12 
The ALPHARMSD action with label a calculates the following quantities:
 Quantity   
 Description  
a.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
a.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
a.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helixg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=9,23,35,50,62,78,89,101,120,135,159,183,202,212,229,253,272,282,297,321,345,362,377,389,400,410
The GYRATION action with label g calculates the following quantities:
 Quantity   
 Description  
g.value
the radius that was computed from the weightsene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingwte: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ene PACEthe frequency for hill addition=999999999 HEIGHTthe heights of the Gaussian hills=2.5 SIGMAthe widths of the Gaussian hills=500.0 FILE a file in which the list of added hills is stored=HILLS_PTWTE BIASFACTORuse well tempered metadynamics and use this bias factor=50.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=367.734

The METAD action with label wte calculates the following quantities:
 Quantity   
 Description  
wte.bias
the instantaneous value of the bias potentialmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=a,g PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=0.4184 SIGMAthe widths of the Gaussian hills=0.15,0.025 FILE a file in which the list of added hills is stored=HILLS_PTMetaDWTE BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=367.734

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a,g,ene,wte.bias,metad.bias STRIDE the frequency with which the quantities of interest should be output=50 FILEthe name of the file on which to output these quantities=COLVAR_MetadWTE

ENDPLUMEDTerminate plumed input. More details