Project ID: plumID:21.036
Source: DHH1N_sampling/PTMetaD-WTE/plumed_CVs_PTMetaD-WTE.dat
Originally used with PLUMED version: 2.5.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTARTMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=Protein.pdba file in pdb format containing a reference structureMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-709the atoms that make up a molecule that you wish to align
ene :ENERGYened :Calculate the total potential energy of the simulation box. More detailsMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=enethe labels of the scalars on which the bias will actPACE=500000000the frequency for hill additionHEIGHT=1.2the heights of the Gaussian hillsSIGMA=2000.0the widths of the Gaussian hillsTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=12use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is storedPrint quantities to a file. More detailsSTRIDE=5000the frequency with which the quantities of interest should be outputARG=ene,ened.biasthe labels of the values that you would like to print to the fileFILE=COLVAR_ENEthe name of the file on which to output these quantities
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 detailsATOMS=5,12,23,42,56,70,84,104,118,132,146,160,174,185,199,213,225,244,256,280,292,316,338,352,362,381,395,416,428,450,472,484,498,524,536,553,567,579,591,607,626,640,654,676,683,697 cv2the numerical indexes for the set of atoms in the groupCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=caFirst list of atomsNN=8The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NNR_0=0.65The r_0 parameter of the switching functionNOPBCignore the periodic boundary conditions when calculating distancesNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=5.0The cutoff for the neighbor listNL_STRIDE=5 :The frequency with which we are updating the atoms in the neighbor list
cg :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 detailsATOMS=27,31,47,61,75,89,109,124,137,151,165,190,205,218,230,249,261,285,297,321,344,367,386,399,403,421,433,455,477,490,503,529,541,559,572,584,595,599,612,631,646,659,688,703 cv3the numerical indexes for the set of atoms in the groupCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=cgFirst list of atomsR_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NNNOPBCignore the periodic boundary conditions when calculating distancesNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=4.0The cutoff for the neighbor listNL_STRIDE=5 :The frequency with which we are updating the atoms in the neighbor list
o1 :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 detailsATOMS=20,39,53,67,81,101,115,129,143,157,171,182,196,210,222,241,253,277,289,313,335,349,359,378,392,425,447,469,481,495,533,550,564,576,588,604,623,637,651,673,680,694 h1 :the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=11,22,41,55,69,83,103,117,131,145,159,173,184,198,212,224,243,255,279,291,315,337,351,361,380,394,427,449,471,483,497,535,552,566,578,590,606,625,639,653,675,682 cv4the numerical indexes for the set of atoms in the groupCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=h1First list of atomsGROUPB=o1Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.20The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NNPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=3.0The cutoff for the neighbor listNL_STRIDE=5 :The frequency with which we are updating the atoms in the neighbor listDIHCOR...Measures the degree of similarity between dihedral angles. This action is a shortcut. More detailsLABEL=cv5a label for the action so that its output can be referenced in the input to other actionsATOMS1=the set of 8 atoms that are being used each of the dihedral correlation values@psi-1,the four atoms that are required to calculate the psi dihedral for residue 1. 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.ATOMS2=the set of 8 atoms that are being used each of the dihedral correlation values@psi-2,the 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.ATOMS3=the set of 8 atoms that are being used each of the dihedral correlation values@psi-3,the 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.ATOMS4=the set of 8 atoms that are being used each of the dihedral correlation values@psi-4,the 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.ATOMS5=the set of 8 atoms that are being used each of the dihedral correlation values@psi-5,the 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.ATOMS6=the set of 8 atoms that are being used each of the dihedral correlation values@psi-6,the 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.ATOMS7=the set of 8 atoms that are being used each of the dihedral correlation values@psi-7,the 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.ATOMS8=the set of 8 atoms that are being used each of the dihedral correlation values@psi-8,the 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.ATOMS9=the set of 8 atoms that are being used each of the dihedral correlation values@psi-9,the 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.ATOMS10=the set of 8 atoms that are being used each of the dihedral correlation values@psi-10,the 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.ATOMS11=the set of 8 atoms that are being used each of the dihedral correlation values@psi-11,the 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.ATOMS12=the set of 8 atoms that are being used each of the dihedral correlation values@psi-12,the 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.ATOMS13=the set of 8 atoms that are being used each of the dihedral correlation values@psi-13,the 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.ATOMS14=the set of 8 atoms that are being used each of the dihedral correlation values@psi-14,the 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.ATOMS15=the set of 8 atoms that are being used each of the dihedral correlation values@psi-15,the 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.ATOMS16=the set of 8 atoms that are being used each of the dihedral correlation values@psi-16,the 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.ATOMS17=the set of 8 atoms that are being used each of the dihedral correlation values@psi-17,the 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.ATOMS18=the set of 8 atoms that are being used each of the dihedral correlation values@psi-18,the 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.ATOMS19=the set of 8 atoms that are being used each of the dihedral correlation values@psi-19,the 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.ATOMS20=the set of 8 atoms that are being used each of the dihedral correlation values@psi-20,the 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.ATOMS21=the set of 8 atoms that are being used each of the dihedral correlation values@psi-21,the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information.@psi-22the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information.ATOMS22=the set of 8 atoms that are being used each of the dihedral correlation values@psi-22,the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information.@psi-23the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information.ATOMS23=the set of 8 atoms that are being used each of the dihedral correlation values@psi-23,the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information.@psi-24the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information.ATOMS24=the set of 8 atoms that are being used each of the dihedral correlation values@psi-24,the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information.@psi-25the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information.ATOMS25=the set of 8 atoms that are being used each of the dihedral correlation values@psi-25,the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information.@psi-26the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information.ATOMS26=the set of 8 atoms that are being used each of the dihedral correlation values@psi-26,the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information.@psi-27the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information.ATOMS27=the set of 8 atoms that are being used each of the dihedral correlation values@psi-27,the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information.@psi-28the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information.ATOMS28=the set of 8 atoms that are being used each of the dihedral correlation values@psi-28,the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information.@psi-29the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information.ATOMS29=the set of 8 atoms that are being used each of the dihedral correlation values@psi-29,the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information.@psi-30the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information.ATOMS30=the set of 8 atoms that are being used each of the dihedral correlation values@psi-30,the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information.@psi-31the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information.ATOMS31=the set of 8 atoms that are being used each of the dihedral correlation values@psi-31,the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information.@psi-32the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information.ATOMS32=the set of 8 atoms that are being used each of the dihedral correlation values@psi-32,the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information.@psi-33the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information.ATOMS33=the set of 8 atoms that are being used each of the dihedral correlation values@psi-33,the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information.@psi-34the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information.ATOMS34=the set of 8 atoms that are being used each of the dihedral correlation values@psi-34,the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information.@psi-35the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information.ATOMS35=the set of 8 atoms that are being used each of the dihedral correlation values@psi-35,the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information.@psi-36the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information.ATOMS36=the set of 8 atoms that are being used each of the dihedral correlation values@psi-36,the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information.@psi-37the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information.ATOMS37=the set of 8 atoms that are being used each of the dihedral correlation values@psi-37,the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information.@psi-38the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information.ATOMS38=the set of 8 atoms that are being used each of the dihedral correlation values@psi-38,the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information.@psi-39the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information.ATOMS39=the set of 8 atoms that are being used each of the dihedral correlation values@psi-39,the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information.@psi-40the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information.ATOMS40=the set of 8 atoms that are being used each of the dihedral correlation values@psi-40,the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information.@psi-41the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information.ATOMS41=the set of 8 atoms that are being used each of the dihedral correlation values@psi-41,the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information.@psi-42the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information.ATOMS42=the set of 8 atoms that are being used each of the dihedral correlation values@psi-42,the four atoms that are required to calculate the psi dihedral for residue 42. Click here for more information.@psi-43the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information.ATOMS43=the set of 8 atoms that are being used each of the dihedral correlation values@psi-43,the four atoms that are required to calculate the psi dihedral for residue 43. Click here for more information.@psi-44the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information.ATOMS44=the set of 8 atoms that are being used each of the dihedral correlation values@psi-44,the four atoms that are required to calculate the psi dihedral for residue 44. Click here for more information.@psi-45... DIHCORthe four atoms that are required to calculate the psi dihedral for residue 45. Click here for more information.GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1-709the group of atoms that you are calculating the Gyration Tensor forLABEL=rga label for the action so that its output can be referenced in the input to other actionsGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=ASPHERICITYThe type of calculation relative to the Gyration Tensor you want to performATOMS=1-709the group of atoms that you are calculating the Gyration Tensor forLABEL=asa label for the action so that its output can be referenced in the input to other actionsGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=KAPPA2The type of calculation relative to the Gyration Tensor you want to performATOMS=1-709the group of atoms that you are calculating the Gyration Tensor forLABEL=kaa label for the action so that its output can be referenced in the input to other actions
cv6ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More detailsRESIDUES=1-45this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedR_0=0.08The r_0 parameter of the switching functionNN=2The n parameter of the switching functionMM=4 : cv7The m parameter of the switching functionANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More detailsRESIDUES=1-45this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedR_0=0.08The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12 : cv8The m parameter of the switching functionPARABETARMSDProbe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More detailsRESIDUES=1-45this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=DRMSDthe manner in which RMSD alignment is performedNN=8The n parameter of the switching functionMM=12The m parameter of the switching functionR_0=0.08 :The r_0 parameter of the switching function
metad :METADUsed to performed metadynamics on one or more collective variables. More detailsARG=cv2,cv3the labels of the scalars on which the bias will actPACE=500the frequency for hill additionHEIGHT=1.2the heights of the Gaussian hillsSIGMA=1.0,1.0the widths of the Gaussian hillsFILE=HILLS_PTWTEa file in which the list of added hills is storedBIASFACTOR=12use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=100,50the lower bounds for the gridGRID_MAX=500,300the upper bounds for the gridGRID_SPACING=0.2,0.2the approximate grid spacing (to be used as an alternative or together with GRID_BIN)CALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]RCT_USTRIDE=10the update stride for calculating the c(t) reweighting factorPrint quantities to a file. More detailsSTRIDE=5000the frequency with which the quantities of interest should be outputFILE=COLVAR_PTWTE_cv2the name of the file on which to output these quantitiesARG=cv2,cv3,cv4,cv5,cv6,cv7,cv8,rg,as,ka,metad.rbiasthe labels of the values that you would like to print to the file