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 onv2.9
tested onmaster
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
STRUCTURE
a file in pdb format containing a reference structure
=NPGins_active.pdb
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the 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:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=745,1016 K745_D855:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the 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
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d
ARG
the input to this function
=K745_E762,K745_D855
VAR
the names to give each of the arguments in the function
=a,b
FUNC
the function you wish to evaluate
=a-b
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
# Distance from active cmap
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file to be included
=cmap_active.dat

# Distance form inactive cmap
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file 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:
ALPHARMSD
Probe the alpha helical content of a protein structure. More details
RESIDUES
this 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_0
The 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