Project ID: plumID:24.027
Source: plumed.dat
Originally used with PLUMED version: 2.7.1
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
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=system/template_md.pdb
The MOLINFO action with label calculates somethingprotThe GROUP action with label prot calculates the following quantities:| Quantity | Type | Description |
| prot | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=1-339
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=prot
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=1000
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed/CVs.dat
# INCLUDE FILE=plumed/CVs.dat
The INCLUDE action with label plumed/CVs.dat calculates somethingALPHARMSDProbe 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=2-22 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=helixThe SECONDARY_STRUCTURE_RMSD action with label helix calculates the following quantities:| Quantity | Type | Description |
| helix | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
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=2-22 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=parThe LOWEST action with label par calculates the following quantities:| Quantity | Type | Description |
| par | vector | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
ANTIBETARMSDProbe the antiparallel 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=2-22 TYPE the manner in which RMSD alignment is performed=DRMSD LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.08 NN=8 MM=12} LABELa label for the action so that its output can be referenced in the input to other actions=antiThe SECONDARY_STRUCTURE_RMSD action with label anti calculates the following quantities:| Quantity | Type | Description |
| anti | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=par.lessthan,anti.lessthan PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=betaThe COMBINE action with label beta calculates the following quantities:| Quantity | Type | Description |
| beta | scalar | a linear compbination |
g1The GROUP action with label g1 calculates the following quantities:| Quantity | Type | Description |
| g1 | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=9,20,42,53,72,86,101,115,137,158,169,186,205,217,232,247,272,278,295,310,329
rgyrThe GYRATION action with label rgyr calculates the following quantities:| Quantity | Type | Description |
| rgyr | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=g1 NOPBC ignore the periodic boundary conditions when calculating distances
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=94,95,96,210,211,212,225,226,227,240,241,242,303,304,305,334,335,336 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=34,35,36,37,129,130,131,132 R_0The r_0 parameter of the switching function=0.6 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=saltThe COORDINATION action with label salt calculates the following quantities:| Quantity | Type | Description |
| salt | scalar | the value of the coordination |
e2eThe DISTANCE action with label e2e calculates the following quantities:| Quantity | Type | Description |
| e2e | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,329 NOPBC ignore the periodic boundary conditions when calculating distances
dihcorThe SUM action with label dihcor calculates the following quantities:| Quantity | Type | Description |
| dihcor | scalar | the sum of all the elements in the input vector |
: DIHCORMeasures the degree of similarity between dihedral angles. More details ...
ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. ,@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.
ATOMS4the set of 8 atoms that are being used each of the dihedral correlation values=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. ,@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.
ATOMS5the set of 8 atoms that are being used each of the dihedral correlation values=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. ,@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.
ATOMS6the set of 8 atoms that are being used each of the dihedral correlation values=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. ,@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.
ATOMS7the set of 8 atoms that are being used each of the dihedral correlation values=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. ,@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.
ATOMS8the set of 8 atoms that are being used each of the dihedral correlation values=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. ,@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.
ATOMS9the set of 8 atoms that are being used each of the dihedral correlation values=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. ,@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.
ATOMS10the set of 8 atoms that are being used each of the dihedral correlation values=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. ,@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.
ATOMS11the set of 8 atoms that are being used each of the dihedral correlation values=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. ,@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.
ATOMS12the set of 8 atoms that are being used each of the dihedral correlation values=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. ,@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.
ATOMS13the set of 8 atoms that are being used each of the dihedral correlation values=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. ,@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.
ATOMS14the set of 8 atoms that are being used each of the dihedral correlation values=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. ,@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.
ATOMS15the set of 8 atoms that are being used each of the dihedral correlation values=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. ,@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.
ATOMS16the set of 8 atoms that are being used each of the dihedral correlation values=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. ,@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.
ATOMS17the set of 8 atoms that are being used each of the dihedral correlation values=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. ,@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.
ATOMS18the set of 8 atoms that are being used each of the dihedral correlation values=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. ,@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information.
ATOMS19the set of 8 atoms that are being used each of the dihedral correlation values=@psi-20the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. ,@psi-21the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information.
NOPBC ignore the periodic boundary conditions when calculating distances
...
zetaThe TORSION action with label zeta calculates the following quantities:| Quantity | Type | Description |
| zeta | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=247,261,263,272 NOPBC ignore the periodic boundary conditions when calculating distances
psiThe TORSION action with label psi calculates the following quantities:| Quantity | Type | Description |
| psi | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=262,272,274,276 NOPBC ignore the periodic boundary conditions when calculating distances
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=55,139,188,269,280,312 R_0The r_0 parameter of the switching function=0.4 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 LABELa label for the action so that its output can be referenced in the input to other actions=hydroThe COORDINATION action with label hydro calculates the following quantities:| Quantity | Type | Description |
| hydro | scalar | the value of the coordination |
# --- End of included input ---
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=helix.lessthan,beta,rgyr,salt,e2e,dihcor,zeta,psi,hydro
HEIGHTthe height of the Gaussian hills, one for all biases=1.2
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=30
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310
SIGMAthe widths of the Gaussian hills=0.73,0.12,0.10,2.47,0.48,1.03,0.93,0.85,0.07
PACEthe frequency for hill addition, one for all biases=500
GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-0.1,-1,-pi,-pi,-1
GRID_MAXthe upper bounds for the grid=100,100,20,400,10,50,pi,pi,10
GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.1,0.01,0.1,0.1,0.01,0.01,0.01,0.01
GRID_WSTRIDEfrequency for dumping the grid=10000
GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.salt,GRID.e2e,GRID.dihcor,GRID.zeta,GRID.psi,GRID.hydro
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS/helix.lessthan,HILLS/beta,HILLS/rgyr,HILLS/salt,HILLS/e2e,HILLS/dihcor,HILLS/zeta,HILLS/psi,HILLS/hydro
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
LABELa label for the action so that its output can be referenced in the input to other actions=pbmetadThe PBMETAD action with label pbmetad calculates the following quantities:| Quantity | Type | Description |
| pbmetad.bias | scalar | the instantaneous value of the bias potential |
... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=helix.lessthan,beta,rgyr,salt,e2e,dihcor,zeta,psi,hydro FILEthe name of the file on which to output these quantities=COLVAR/COLVAR_PBMETAD STRIDE the frequency with which the quantities of interest should be output=500
ENDPLUMEDTerminate plumed input. More details
