PLUMED-NEST-TEST-SITE

Project ID: plumID:25.008
Source: chignolin/training/metad_for_training/plumed.dat
Originally used with PLUMED version: 2.10
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

# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 


#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=chignolin-ref.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 ENTITY0the atoms that make up a molecule that you wish to align=1-166

# Select Calpha
PROTEINThe GROUP action with label PROTEIN calculates the following quantities:
 Quantity   
 Type   
 Description  
PROTEIN
atoms
indices of atoms specified in GROUP: 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=1-166
CAThe GROUP action with label CA calculates the following quantities:
 Quantity   
 Type   
 Description  
CA
atoms
indices of atoms specified in GROUP: 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=5,26,47,61,73,88,102,109,123,147

rmsd_caThe RMSD action with label rmsd_ca calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_ca
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=chignolin-ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0


metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=rmsd_ca
  PACEthe frequency for hill addition=500
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  HEIGHTthe heights of the Gaussian hills=0.6
  SIGMAthe widths of the Gaussian hills=0.02
...
metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=rmsd_ca
  PACEthe frequency for hill addition=500
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  HEIGHTthe heights of the Gaussian hills=0.6
  SIGMAthe widths of the Gaussian hills=0.02
 FILE a file in which the list of added hills is stored=HILLS
...

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