PLUMED-NEST

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. 
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=hrex_total_renum.pdb


The MOLINFO action with label  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=1-930
The GROUP action with label n calculates somethingh: 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=@hydrogensall hydrogen atoms. Click here for more information. 
The GROUP action with label h calculates somethingnnh: 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=n REMOVEremove these atoms from the list=h

The GROUP action with label nnh 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=nnh

ene: ENERGYCalculate the total potential energy of the simulation box. More details 
The ENERGY action with label ene calculates somethingmeta: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ene SIGMAthe widths of the Gaussian hills=500 HEIGHTthe heights of the Gaussian hills=2.4 BIASFACTORuse well tempered metadynamics and use this bias factor=25 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=-900000 GRID_MAXthe upper bounds for the grid=-400000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=339

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.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=ene FILEthe name of the file on which to output these quantities=COLVAR_metad STRIDE the frequency with which the quantities of interest should be output=100