Project ID: plumID:20.020
Source: plumed.dat
Originally used with PLUMED version: 2.2
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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed_cv.dat
# INCLUDE FILE=plumed_cv.dat
The INCLUDE action with label plumed_cv.dat 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=trp.pdb
The MOLINFO action with label calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details RESIDUESthis command specifies that the backbone atoms in a set of residues all must be aligned=all MOLTYPEthe type of molecule that is under study=protein
rgThe GYRATION action with label rg calculates the following quantities:| Quantity | Type | Description |
| rg | 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=5,19,38,59,78,95,119,138,160,172,179,194,200,211,222,229,261,275,289,295 NOPBC ignore the periodic boundary conditions when calculating distances
COORDINATIONCalculate coordination numbers. More details ...
GROUPAFirst list of atoms=16,35,56,75,92,116,135,157,169,176,183,197,208,219,226,250,264,278,292
GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=18,37,58,77,94,118,137,159,171,178,199,210,221,228,294
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.25 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 LABELa label for the action so that its output can be referenced in the input to other actions=hbThe COORDINATION action with label hb calculates the following quantities:| Quantity | Type | Description |
| hb | scalar | the value of the coordination |
NOPBC ignore the periodic boundary conditions when calculating distances
... COORDINATION
COORDINATIONCalculate coordination numbers. More details ...
GROUPAFirst list of atoms=24,100,124,188,255,269,283
NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 R_0The r_0 parameter of the switching function=0.5 LABELa label for the action so that its output can be referenced in the input to other actions=hcThe COORDINATION action with label hc calculates the following quantities:| Quantity | Type | Description |
| hc | scalar | the value of the coordination |
NOPBC ignore the periodic boundary conditions when calculating distances
... COORDINATION
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. REFERENCE1the reference values for each of the torsional angles=-1.0
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. REFERENCE2the reference values for each of the torsional angles=-0.82
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. REFERENCE3the reference values for each of the torsional angles=-1.0
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. REFERENCE4the reference values for each of the torsional angles=-0.82
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. REFERENCE5the reference values for each of the torsional angles=-1.0
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. REFERENCE6the reference values for each of the torsional angles=-0.82
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. REFERENCE7the reference values for each of the torsional angles=-1.0
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. REFERENCE8the reference values for each of the torsional angles=-0.82
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. REFERENCE9the reference values for each of the torsional angles=-1.0
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. REFERENCE10the reference values for each of the torsional angles=-0.82
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. REFERENCE11the reference values for each of the torsional angles=-1.0
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. REFERENCE12the reference values for each of the torsional angles=-0.82
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. REFERENCE14the reference values for each of the torsional angles=-0.82
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. REFERENCE16the reference values for each of the torsional angles=-0.82
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. REFERENCE18the reference values for each of the torsional angles=-0.82
ATOMS19the atoms involved for each of the torsions you wish to calculate=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. REFERENCE20the reference values for each of the torsional angles=-0.82
ATOMS21the atoms involved for each of the torsions you wish to calculate=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. REFERENCE22the reference values for each of the torsional angles=-0.82
ATOMS23the atoms involved for each of the torsions you wish to calculate=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. REFERENCE24the reference values for each of the torsional angles=-0.82
ATOMS25the atoms involved for each of the torsions you wish to calculate=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. REFERENCE25the reference values for each of the torsional angles=-1.0
ATOMS26the atoms involved for each of the torsions you wish to calculate=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. REFERENCE26the reference values for each of the torsional angles=-0.82
ATOMS27the atoms involved for each of the torsions you wish to calculate=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. REFERENCE27the reference values for each of the torsional angles=-1.0
ATOMS28the atoms involved for each of the torsions you wish to calculate=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. REFERENCE28the reference values for each of the torsional angles=-0.82
ATOMS29the atoms involved for each of the torsions you wish to calculate=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. REFERENCE29the reference values for each of the torsional angles=-1.0
ATOMS30the atoms involved for each of the torsions you wish to calculate=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. REFERENCE30the reference values for each of the torsional angles=-0.82
ATOMS31the atoms involved for each of the torsions you wish to calculate=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. REFERENCE31the reference values for each of the torsional angles=-1.0
ATOMS32the atoms involved for each of the torsions you wish to calculate=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. REFERENCE32the reference values for each of the torsional angles=-0.82
ATOMS33the atoms involved for each of the torsions you wish to calculate=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. REFERENCE33the reference values for each of the torsional angles=-1.0
ATOMS34the atoms involved for each of the torsions you wish to calculate=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. REFERENCE34the reference values for each of the torsional angles=-0.82
ATOMS35the atoms involved for each of the torsions you wish to calculate=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. REFERENCE35the reference values for each of the torsional angles=-1.0
ATOMS36the atoms involved for each of the torsions you wish to calculate=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. REFERENCE36the reference values for each of the torsional angles=-0.82
LABELa label for the action so that its output can be referenced in the input to other actions=helixThe SUM action with label helix calculates the following quantities:| Quantity | Type | Description |
| helix | scalar | the sum of all the elements in the input vector |
... ALPHABETA
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. REFERENCE1the reference values for each of the torsional angles=-1.396
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. REFERENCE2the reference values for each of the torsional angles=2.618
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. REFERENCE3the reference values for each of the torsional angles=-1.396
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. REFERENCE4the reference values for each of the torsional angles=2.618
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. REFERENCE5the reference values for each of the torsional angles=-1.396
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. REFERENCE6the reference values for each of the torsional angles=2.618
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. REFERENCE7the reference values for each of the torsional angles=-1.396
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. REFERENCE8the reference values for each of the torsional angles=2.618
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. REFERENCE9the reference values for each of the torsional angles=-1.396
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. REFERENCE10the reference values for each of the torsional angles=2.618
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. REFERENCE11the reference values for each of the torsional angles=-1.396
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. REFERENCE12the reference values for each of the torsional angles=2.618
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. REFERENCE13the reference values for each of the torsional angles=-1.396
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. REFERENCE14the reference values for each of the torsional angles=2.618
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. REFERENCE15the reference values for each of the torsional angles=-1.396
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. REFERENCE16the reference values for each of the torsional angles=2.618
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. REFERENCE17the reference values for each of the torsional angles=-1.396
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-10the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. REFERENCE18the reference values for each of the torsional angles=2.618
ATOMS19the atoms involved for each of the torsions you wish to calculate=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information. REFERENCE19the reference values for each of the torsional angles=-1.396
ATOMS20the atoms involved for each of the torsions you wish to calculate=@psi-11the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. REFERENCE20the reference values for each of the torsional angles=2.618
ATOMS21the atoms involved for each of the torsions you wish to calculate=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information. REFERENCE21the reference values for each of the torsional angles=-1.396
ATOMS22the atoms involved for each of the torsions you wish to calculate=@psi-12the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. REFERENCE22the reference values for each of the torsional angles=2.618
ATOMS23the atoms involved for each of the torsions you wish to calculate=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information. REFERENCE23the reference values for each of the torsional angles=-1.396
ATOMS24the atoms involved for each of the torsions you wish to calculate=@psi-13the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. REFERENCE24the reference values for each of the torsional angles=2.618
ATOMS25the atoms involved for each of the torsions you wish to calculate=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information. REFERENCE25the reference values for each of the torsional angles=-1.396
ATOMS26the atoms involved for each of the torsions you wish to calculate=@psi-14the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. REFERENCE26the reference values for each of the torsional angles=2.618
ATOMS27the atoms involved for each of the torsions you wish to calculate=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information. REFERENCE27the reference values for each of the torsional angles=-1.396
ATOMS28the atoms involved for each of the torsions you wish to calculate=@psi-15the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. REFERENCE28the reference values for each of the torsional angles=2.618
ATOMS29the atoms involved for each of the torsions you wish to calculate=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information. REFERENCE29the reference values for each of the torsional angles=-1.396
ATOMS30the atoms involved for each of the torsions you wish to calculate=@psi-16the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. REFERENCE30the reference values for each of the torsional angles=2.618
ATOMS31the atoms involved for each of the torsions you wish to calculate=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information. REFERENCE31the reference values for each of the torsional angles=-1.396
ATOMS32the atoms involved for each of the torsions you wish to calculate=@psi-17the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. REFERENCE32the reference values for each of the torsional angles=2.618
ATOMS33the atoms involved for each of the torsions you wish to calculate=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information. REFERENCE33the reference values for each of the torsional angles=-1.396
ATOMS34the atoms involved for each of the torsions you wish to calculate=@psi-18the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. REFERENCE34the reference values for each of the torsional angles=2.618
ATOMS35the atoms involved for each of the torsions you wish to calculate=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information. REFERENCE35the reference values for each of the torsional angles=-1.396
ATOMS36the atoms involved for each of the torsions you wish to calculate=@psi-19the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. REFERENCE36the reference values for each of the torsional angles=2.618
LABELa label for the action so that its output can be referenced in the input to other actions=betaThe SUM action with label beta calculates the following quantities:| Quantity | Type | Description |
| beta | scalar | the sum of all the elements in the input vector |
... ALPHABETA
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=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. ,@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.
ATOMS2the 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. ,@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. 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.
ATOMS4the 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. ,@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.
ATOMS5the set of 8 atoms that are being used each of the dihedral correlation values=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. 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.
ATOMS6the 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. ,@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.
ATOMS7the set of 8 atoms that are being used each of the dihedral correlation values=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. 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.
ATOMS8the 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. ,@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.
ATOMS9the set of 8 atoms that are being used each of the dihedral correlation values=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. 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.
ATOMS10the 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. ,@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.
ATOMS11the set of 8 atoms that are being used each of the dihedral correlation values=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. 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.
ATOMS12the 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. ,@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.
ATOMS13the set of 8 atoms that are being used each of the dihedral correlation values=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. 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.
ATOMS14the 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. ,@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.
ATOMS15the set of 8 atoms that are being used each of the dihedral correlation values=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. 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.
ATOMS16the 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. ,@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.
ATOMS17the set of 8 atoms that are being used each of the dihedral correlation values=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. 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.
ATOMS18the 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. ,@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.
ATOMS19the set of 8 atoms that are being used each of the dihedral correlation values=@phi-11the four atoms that are required to calculate the phi dihedral for residue 11. 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.
ATOMS20the 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. ,@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.
ATOMS21the set of 8 atoms that are being used each of the dihedral correlation values=@phi-12the four atoms that are required to calculate the phi dihedral for residue 12. 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.
ATOMS22the 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. ,@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.
ATOMS23the set of 8 atoms that are being used each of the dihedral correlation values=@phi-13the four atoms that are required to calculate the phi dihedral for residue 13. 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.
ATOMS24the 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. ,@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.
ATOMS25the set of 8 atoms that are being used each of the dihedral correlation values=@phi-14the four atoms that are required to calculate the phi dihedral for residue 14. 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.
ATOMS26the 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. ,@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.
ATOMS27the set of 8 atoms that are being used each of the dihedral correlation values=@phi-15the four atoms that are required to calculate the phi dihedral for residue 15. 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.
ATOMS28the 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. ,@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.
ATOMS29the set of 8 atoms that are being used each of the dihedral correlation values=@phi-16the four atoms that are required to calculate the phi dihedral for residue 16. 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.
ATOMS30the 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. ,@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.
ATOMS31the set of 8 atoms that are being used each of the dihedral correlation values=@phi-17the four atoms that are required to calculate the phi dihedral for residue 17. 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.
ATOMS32the 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. ,@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.
ATOMS33the set of 8 atoms that are being used each of the dihedral correlation values=@phi-18the four atoms that are required to calculate the phi dihedral for residue 18. 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.
ATOMS34the 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. ,@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.
ATOMS35the set of 8 atoms that are being used each of the dihedral correlation values=@phi-19the four atoms that are required to calculate the phi dihedral for residue 19. 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.
LABELa label for the action so that its output can be referenced in the input to other actions=dihThe SUM action with label dih calculates the following quantities:| Quantity | Type | Description |
| dih | scalar | the sum of all the elements in the input vector |
... DIHCOR
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=rg,hb,hc,helix,beta,dih STRIDE the frequency with which the quantities of interest should be output=500
# --- End of included input ---
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=rg,hb,hc,helix,beta,dih
PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=8.0 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
SIGMAthe widths of the Gaussian hills=0.01,0.6,0.3,0.4,0.3,0.6
GRID_MINthe lower bounds for the grid=0.4,0.0,0.0,0.0,0.0,0.0
GRID_MAXthe upper bounds for the grid=2.0,100.0,25.0,40.0,40.0,40.0
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_rg,HILLS_hb,HILLS_hc,HILLS_helix,HILLS_beta,HILLS_dih LABELa label for the action so that its output can be referenced in the input to other actions=metadThe PBMETAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
... PBMETAD
