Project ID: plumID:21.027
Source: D770-N771insNPG/plumed.dat
Originally used with PLUMED version: 2.4
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
tested onv2.10
tested onmaster
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=NPGins_active.pdb 
WHOLEMOLECULESThis 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=1-4752
# Distances describing the two saltbridges K745(NZ):E762(CD) and K745(ΝΖ):D855(CG)
# that reflect the conformation of the aC helix
# (CVs described in Ludo's paper doi:10.1073/pnas.1221953110)
K745_E762: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=745,1016
K745_D855: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=745,2556

# Distance between the two distance
# When both saltbridges are formed, the distance between the two distances (CV)
# is close to 0. This CV is able to characterise the displacement of the fuctionally important
# E762 located in the aC helix of the N-lobe in its transition from the so-called "aC-in" to "aC-out" conformation
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=d
    ARGthe values input to this function=K745_E762,K745_D855
    VARthe names to give each of the arguments in the function=a,b
    FUNCthe function you wish to evaluate=a-b
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

# Distance from active cmap INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cmap_active.dat
# Distance form inactive cmap INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cmap_inactive.dat
# Monitor the helical content of the aC-helix to probe # its intrisically disordered nature in the monomeric form armsd: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=751-773 TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12