PLUMED-NEST

Click on the labels of the actions for more information on what each action computes

#RESTART

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=1-1800

The WHOLEMOLECULES action with label  calculates somethingMOLINFOThis 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=../em_ww.pdb


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## Rg of CA atoms

ca_atoms: 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 NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=CA      NDX_FILEthe name of index file (gromacs syntax)=../ind_CA.ndx

The GROUP action with label ca_atoms calculates somethingrg_ca: GYRATIONCalculate the radius of gyration, or other properties related to it. More details  TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS  ATOMSthe group of atoms that you are calculating the Gyration Tensor for=ca_atoms NOPBC ignore the periodic boundary conditions when calculating distances

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## Fraction of CA native contacts

The GYRATION action with label rg_ca calculates the following quantities:
 Quantity   
 Description  
rg_ca.value
the radius that was computed from the weightsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=../plumed_cmap.dat 

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## Total alpha-helical content

alpha: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=120-228

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## Distance between COM of H1 and COM of disulfide bridge


The ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Description  
alpha.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
alpha.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helixsg: 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 NDX_FILEthe name of index file (gromacs syntax)=../ind_com_h1_sg.ndx   NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=SG
The GROUP action with label sg calculates somethingh1: 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 NDX_FILEthe name of index file (gromacs syntax)=../ind_com_h1_sg.ndx   NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=H1_woH

The GROUP action with label h1 calculates somethingcom_sg: COMCalculate the center of mass for a group of atoms. More details  ATOMSthe list of atoms which are involved the virtual atom's definition=sg NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label com_sg calculates somethingcom_h1: COMCalculate the center of mass for a group of atoms. More details  ATOMSthe list of atoms which are involved the virtual atom's definition=h1 NOPBC ignore the periodic boundary conditions when calculating distances

The COM action with label com_h1 calculates somethingDUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mcfile

d_h1_sg: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com_sg,com_h1 NOPBC ignore the periodic boundary conditions when calculating distances

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## CA contacts between S1H1S2 and H2H3 subdomains

The DISTANCE action with label d_h1_sg calculates the following quantities:
 Quantity   
 Description  
d_h1_sg.value
the DISTANCE between this pair of atomsgrp_s1h1s2_ca: 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  NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=r_120-166_&_CA   NDX_FILEthe name of index file (gromacs syntax)=../ind_CA.ndx

The GROUP action with label grp_s1h1s2_ca calculates somethinggrp_h2h3_ca: 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  NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=r_174-228_&_CA     NDX_FILEthe name of index file (gromacs syntax)=../ind_CA.ndx

The GROUP action with label grp_h2h3_ca calculates somethingsca: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=grp_s1h1s2_ca  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=grp_h2h3_ca  R_0The r_0 parameter of the switching function=0.8 NOPBC ignore the periodic boundary conditions when calculating distances

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## SIGMA values for the CVs were chosen as half of the standard deviation
## calculated from the unbiased simulation. The bias factor was set to
## 10*sqrt(number of CVs). 

The COORDINATION action with label sca calculates the following quantities:
 Quantity   
 Description  
sca.value
the value of the coordinationpb: PBMETADUsed to performed Parallel Bias metadynamics. More details  ARGthe labels of the scalars on which the bias will act=rg_ca,alpha,d_h1_sg,cmap,sca  SIGMAthe widths of the Gaussian hills=0.006,0.48,0.016,0.0066,2.0  PACEthe frequency for hill addition, one for all biases=1000  HEIGHTthe height of the Gaussian hills, one for all biases=1.0  BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=22  GRID_MINthe lower bounds for the grid=0,0,0,0,0  GRID_MAXthe upper bounds for the grid=14,100,12,1.8,300  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300  FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_rg,HILLS_alpha,HILLS_dh1sg,HILLS_cmap,HILLS_sca  WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR WALKERS_DIRshared directory with the hills files from all the walkers=../

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The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.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=*  FILEthe name of the file on which to output these quantities=COLVAR_pb  STRIDE the frequency with which the quantities of interest should be output=500