PLUMED-NEST

Project ID: plumID:25.023
Source: monomer/bias_16/plumed.dat
Originally used with PLUMED version: 2.8
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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingrmsda: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=prot_ref_a.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL   

The RMSD action with label rmsda calculates the following quantities:
 Quantity   
 Description  
rmsda.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=rmsda PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=2.577483412 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=10.0 BIASFACTORuse well tempered metadynamics and use this bias factor=16.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.0 RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES

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=rmsda,metad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500