PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV7/plumed.6.dat
Originally used with PLUMED version: 2.5.2
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=Protein.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein

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=1-709

RANDOM_EXCHANGESSet random pattern for exchanges. More details

cv7: PARABETARMSDProbe the parallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=1-45 TYPE the manner in which RMSD alignment is performed=DRMSD NN The n parameter of the switching function=8 MM The m parameter of the switching function=12 R_0The r_0 parameter of the switching function=0.08 NOPBC ignore the periodic boundary conditions

The PARABETARMSD action with label cv7 calculates the following quantities:
 Quantity   
 Description  
cv7.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
cv7.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
cv7.value
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheetlwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv7 ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=30.0
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv7 ATthe positions of the wall=8.0 KAPPAthe force constant for the wall=30.0

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this 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=cv7 PACEthe frequency for hill addition=2500 HEIGHTthe heights of the Gaussian hills=0.3 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=30.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.025

#PRINT STRIDE=10 ARG=cv7,metad.bias FILE=COLVAR
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 STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cv7,metad.bias,uwall.bias,lwall.bias FILEthe name of the file on which to output these quantities=COLVAR