Project ID: plumID:22.023
Source: ANALYSIS/plumed_analysis.dat
Originally used with PLUMED version: 2.6-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=structure.pdba file in pdb format containing a reference structure
# define all heavy atoms using GROMACS index file protein-h: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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein-H protein:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein system:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Systemthe name of the group to be imported (gromacs syntax) - first group found is used by default
# make protein whole: add reference position of first heavy atom (in nm)WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-537the atoms that make up a molecule that you wish to alignENTITY1=538-1074the atoms that make up a molecule that you wish to alignENTITY2=1075-1611the atoms that make up a molecule that you wish to alignENTITY3=1612-2148the atoms that make up a molecule that you wish to alignENTITY4=2149-2685the atoms that make up a molecule that you wish to alignENTITY5=2686-3222the atoms that make up a molecule that you wish to alignENTITY6=3223-3759the atoms that make up a molecule that you wish to alignENTITY7=3760-4296the atoms that make up a molecule that you wish to alignENTITY8=4297-4833the atoms that make up a molecule that you wish to alignENTITY9=4834-5370the atoms that make up a molecule that you wish to alignENTITY10=5371-5907the atoms that make up a molecule that you wish to alignENTITY11=5908-6444the atoms that make up a molecule that you wish to alignENTITY12=6445-6981the atoms that make up a molecule that you wish to alignENTITY13=6982-7518the atoms that make up a molecule that you wish to alignENTITY14=7519-8055the atoms that make up a molecule that you wish to alignENTITY15=8056-8592the atoms that make up a molecule that you wish to alignADDREFERENCEREF0=7.977,12.295,6.939 REF1=11.453,6.771,7.163 REF2=7.857,12.19,7.532 REF3=11.438,6.79,7.776 REF4=7.661,12.18,8.36 REF5=11.474,6.687,8.62 REF6=7.569,12.049,8.69 REF7=11.475,6.772,8.977 REF8=7.658,11.999,9.265 REF9=11.274,6.704,9.522 REF10=7.191,11.806,9.51 REF11=11.639,6.928,9.885 REF12=7.515,11.723,10.332 REF13=11.16,6.807,10.622 REF14=7.347,11.62,10.843 REF15=11.207,6.847,11.166Define the reference position of the first atom of each entity using a PDB file
# Constrain the protein CA protofibril coreRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=fibril_core.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedLABEL=rmsda label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsdthe arguments on which the bias is actingAT=0.3the positions of the wallKAPPA=0.0the force constant for the wallEXP=3the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=rmsdwalla label for the action so that its output can be referenced in the input to other actions
# Disulfide dihedral (CYS2:CB,CYS2:S,CYS7:S,CYS7:CB) disulf1:TORSIONCalculate a torsional angle. More detailsATOMS=29,32,94,91 disulf2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=1103,1106,1168,1165 disulf3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=2177,2180,2242,2239 disulf4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=3251,3254,3316,3313 disulf5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=4325,4328,4390,4387 disulf6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=5399,5402,5464,5461 disulf7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=6473,6476,6538,6535 disulf8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=7547,7550,7612,7609the four atoms involved in the torsional angle
ph1:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-223ph2:the four atoms that are required to calculate the phi dihedral for residue 223. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-224ph3:the four atoms that are required to calculate the phi dihedral for residue 224. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-225ph4:the four atoms that are required to calculate the phi dihedral for residue 225. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-226ph5:the four atoms that are required to calculate the phi dihedral for residue 226. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-227ph6:the four atoms that are required to calculate the phi dihedral for residue 227. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-228ph7:the four atoms that are required to calculate the phi dihedral for residue 228. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-229ph8:the four atoms that are required to calculate the phi dihedral for residue 229. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-230ph9:the four atoms that are required to calculate the phi dihedral for residue 230. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-231ph10:the four atoms that are required to calculate the phi dihedral for residue 231. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-232ph11:the four atoms that are required to calculate the phi dihedral for residue 232. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-233ph12:the four atoms that are required to calculate the phi dihedral for residue 233. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-234the four atoms that are required to calculate the phi dihedral for residue 234. Click here for more information.
ps1:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-223ps2:the four atoms that are required to calculate the psi dihedral for residue 223. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-224ps3:the four atoms that are required to calculate the psi dihedral for residue 224. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-225ps4:the four atoms that are required to calculate the psi dihedral for residue 225. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-226ps5:the four atoms that are required to calculate the psi dihedral for residue 226. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-227ps6:the four atoms that are required to calculate the psi dihedral for residue 227. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-228ps7:the four atoms that are required to calculate the psi dihedral for residue 228. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-229ps8:the four atoms that are required to calculate the psi dihedral for residue 229. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-230ps9:the four atoms that are required to calculate the psi dihedral for residue 230. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-231ps10:the four atoms that are required to calculate the psi dihedral for residue 231. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-232ps11:the four atoms that are required to calculate the psi dihedral for residue 232. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-233ps12:the four atoms that are required to calculate the psi dihedral for residue 233. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-234the four atoms that are required to calculate the psi dihedral for residue 234. Click here for more information.
ph13:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-297ph14:the four atoms that are required to calculate the phi dihedral for residue 297. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-299ph15:the four atoms that are required to calculate the phi dihedral for residue 299. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-299ph16:the four atoms that are required to calculate the phi dihedral for residue 299. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-300ph17:the four atoms that are required to calculate the phi dihedral for residue 300. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-301ph18:the four atoms that are required to calculate the phi dihedral for residue 301. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-302ph19:the four atoms that are required to calculate the phi dihedral for residue 302. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-303ph20:the four atoms that are required to calculate the phi dihedral for residue 303. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-304ph21:the four atoms that are required to calculate the phi dihedral for residue 304. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-305ph22:the four atoms that are required to calculate the phi dihedral for residue 305. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-306ph23:the four atoms that are required to calculate the phi dihedral for residue 306. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-307ph24:the four atoms that are required to calculate the phi dihedral for residue 307. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@phi-308the four atoms that are required to calculate the phi dihedral for residue 308. Click here for more information.
ps13:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-297ps14:the four atoms that are required to calculate the psi dihedral for residue 297. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-299ps15:the four atoms that are required to calculate the psi dihedral for residue 299. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-299ps16:the four atoms that are required to calculate the psi dihedral for residue 299. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-300ps17:the four atoms that are required to calculate the psi dihedral for residue 300. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-301ps18:the four atoms that are required to calculate the psi dihedral for residue 301. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-302ps19:the four atoms that are required to calculate the psi dihedral for residue 302. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-303ps20:the four atoms that are required to calculate the psi dihedral for residue 303. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-304ps21:the four atoms that are required to calculate the psi dihedral for residue 304. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-305ps22:the four atoms that are required to calculate the psi dihedral for residue 305. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-306ps23:the four atoms that are required to calculate the psi dihedral for residue 306. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-307ps24:the four atoms that are required to calculate the psi dihedral for residue 307. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@psi-308the four atoms that are required to calculate the psi dihedral for residue 308. Click here for more information.
#UNBIASED disulf9:TORSIONCalculate a torsional angle. More detailsATOMS=566,569,631,628 disulf10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=1640,1643,1705,1702 disulf11:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=2714,2717,2779,2776 disulf12:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=3788,3791,3853,3850 disulf13:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=4862,4865,4927,4924 disulf14:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=5936,5939,6001,5998 disulf15:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=7010,7013,7075,7072 disulf16:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=8084,8087,8149,8146 ###############################the four atoms involved in the torsional angle
# Tail definitions tail1: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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail1 tail3:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail3 tail5:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail5 tail7:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail7 tail9:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail9 tail11:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail11 tail13:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail13 tail15:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail15the name of the group to be imported (gromacs syntax) - first group found is used by default
#UNBIASED Tail definitions tail2: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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail2 tail4:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail4 tail6:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail6 tail8:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail8 tail10:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail10 tail12:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail12 tail14:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail14 tail16:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=tail16the name of the group to be imported (gromacs syntax) - first group found is used by default
# Inter-tail contacts # Theoretical maximum: 3828 con1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=tail1First list of atomsGROUPB=tail3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con2:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail3First list of atomsGROUPB=tail5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con3:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail5First list of atomsGROUPB=tail7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con4:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail7First list of atomsGROUPB=tail9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con5:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail9First list of atomsGROUPB=tail11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con6:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail11First list of atomsGROUPB=tail13Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con7:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail13First list of atomsGROUPB=tail15Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8The r_0 parameter of the switching function
#UNBIASED con8:COORDINATIONCalculate coordination numbers. More detailsGROUPA=tail2First list of atomsGROUPB=tail4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con9:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail4First list of atomsGROUPB=tail6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con10:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail6First list of atomsGROUPB=tail8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con11:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail8First list of atomsGROUPB=tail10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con12:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail10First list of atomsGROUPB=tail12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con13:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail12First list of atomsGROUPB=tail14Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 con14:The r_0 parameter of the switching functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=tail14First list of atomsGROUPB=tail16Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.8 #################The r_0 parameter of the switching function
# 1 com-cys2-1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-2com-cys7-1:the protein/dna/rna backbone atoms in residue 2. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-7com-as14-1:the protein/dna/rna backbone atoms in residue 7. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-14com-as31-1:the protein/dna/rna backbone atoms in residue 14. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-31# 2 com-cys2-2:the protein/dna/rna backbone atoms in residue 31. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-76com-cys7-2:the protein/dna/rna backbone atoms in residue 76. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-81com-as14-2:the protein/dna/rna backbone atoms in residue 81. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-88com-as31-2:the protein/dna/rna backbone atoms in residue 88. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-105# 3 com-cys2-3:the protein/dna/rna backbone atoms in residue 105. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-150com-cys7-3:the protein/dna/rna backbone atoms in residue 150. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-155com-as14-3:the protein/dna/rna backbone atoms in residue 155. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-162com-as31-3:the protein/dna/rna backbone atoms in residue 162. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-179# 4 com-cys2-4:the protein/dna/rna backbone atoms in residue 179. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-224com-cys7-4:the protein/dna/rna backbone atoms in residue 224. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-229com-as14-4:the protein/dna/rna backbone atoms in residue 229. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-236com-as31-4:the protein/dna/rna backbone atoms in residue 236. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-253# 5 com-cys2-5:the protein/dna/rna backbone atoms in residue 253. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-298com-cys7-5:the protein/dna/rna backbone atoms in residue 298. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-303com-as14-5:the protein/dna/rna backbone atoms in residue 303. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-310com-as31-5:the protein/dna/rna backbone atoms in residue 310. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-327# 6 com-cys2-6:the protein/dna/rna backbone atoms in residue 327. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-372com-cys7-6:the protein/dna/rna backbone atoms in residue 372. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-377com-as14-6:the protein/dna/rna backbone atoms in residue 377. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-384com-as31-6:the protein/dna/rna backbone atoms in residue 384. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-401# 7 com-cys2-7:the protein/dna/rna backbone atoms in residue 401. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-446com-cys7-7:the protein/dna/rna backbone atoms in residue 446. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-451com-as14-7:the protein/dna/rna backbone atoms in residue 451. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-458com-as31-7:the protein/dna/rna backbone atoms in residue 458. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-475# 8 com-cys2-8:the protein/dna/rna backbone atoms in residue 475. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-520com-cys7-8:the protein/dna/rna backbone atoms in residue 520. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-525com-as14-8:the protein/dna/rna backbone atoms in residue 525. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-532com-as31-8:the protein/dna/rna backbone atoms in residue 532. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-549the protein/dna/rna backbone atoms in residue 549. Click here for more information.
# Tail torsion (CYS2:CA,CYS7:CA,ASN14:CA,ASN31:CA) tor1:TORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-1,com-cys7-1,com-as14-1,com-as31-1 tor2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-2,com-cys7-2,com-as14-2,com-as31-2 tor3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-3,com-cys7-3,com-as14-3,com-as31-3 tor4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-4,com-cys7-4,com-as14-4,com-as31-4 tor5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-5,com-cys7-5,com-as14-5,com-as31-5 tor6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-6,com-cys7-6,com-as14-6,com-as31-6 tor7:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-7,com-cys7-7,com-as14-7,com-as31-7 tor8:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-8,com-cys7-8,com-as14-8,com-as31-8the four atoms involved in the torsional angle
#UNBIASED # 1 com-cys2-9:COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-39com-cys7-9:the protein/dna/rna backbone atoms in residue 39. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-44com-as14-9:the protein/dna/rna backbone atoms in residue 44. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-51com-as31-9:the protein/dna/rna backbone atoms in residue 51. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-68# 2 com-cys2-10:the protein/dna/rna backbone atoms in residue 68. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-113com-cys7-10:the protein/dna/rna backbone atoms in residue 113. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-118com-as14-10:the protein/dna/rna backbone atoms in residue 118. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-125com-as31-10:the protein/dna/rna backbone atoms in residue 125. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-142# 3 com-cys2-11:the protein/dna/rna backbone atoms in residue 142. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-187com-cys7-11:the protein/dna/rna backbone atoms in residue 187. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-192com-as14-11:the protein/dna/rna backbone atoms in residue 192. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-199com-as31-11:the protein/dna/rna backbone atoms in residue 199. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-216# 4 com-cys2-12:the protein/dna/rna backbone atoms in residue 216. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-261com-cys7-12:the protein/dna/rna backbone atoms in residue 261. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-266com-as14-12:the protein/dna/rna backbone atoms in residue 266. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-273com-as31-12:the protein/dna/rna backbone atoms in residue 273. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-290# 5 com-cys2-13:the protein/dna/rna backbone atoms in residue 290. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-335com-cys7-13:the protein/dna/rna backbone atoms in residue 335. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-340com-as14-13:the protein/dna/rna backbone atoms in residue 340. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-347com-as31-13:the protein/dna/rna backbone atoms in residue 347. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-364# 6 com-cys2-14:the protein/dna/rna backbone atoms in residue 364. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-409com-cys7-14:the protein/dna/rna backbone atoms in residue 409. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-414com-as14-14:the protein/dna/rna backbone atoms in residue 414. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-421com-as31-14:the protein/dna/rna backbone atoms in residue 421. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-438# 7 com-cys2-15:the protein/dna/rna backbone atoms in residue 438. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-483com-cys7-15:the protein/dna/rna backbone atoms in residue 483. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-488com-as14-15:the protein/dna/rna backbone atoms in residue 488. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-495com-as31-15:the protein/dna/rna backbone atoms in residue 495. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-512# 8 com-cys2-16:the protein/dna/rna backbone atoms in residue 512. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-557com-cys7-16:the protein/dna/rna backbone atoms in residue 557. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-562com-as14-16:the protein/dna/rna backbone atoms in residue 562. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-569com-as31-16:the protein/dna/rna backbone atoms in residue 569. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@back-586the protein/dna/rna backbone atoms in residue 586. Click here for more information.
# Tail torsion (CYS2:CA,CYS7:CA,ASN14:CA,ASN31:CA) tor9:TORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-9,com-cys7-9,com-as14-9,com-as31-9 tor10:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-10,com-cys7-10,com-as14-10,com-as31-10 tor11:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-11,com-cys7-11,com-as14-11,com-as31-11 tor12:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-12,com-cys7-12,com-as14-12,com-as31-12 tor13:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-13,com-cys7-13,com-as14-13,com-as31-13 tor14:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-14,com-cys7-14,com-as14-14,com-as31-14 tor15:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-15,com-cys7-15,com-as14-15,com-as31-15 tor16:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=com-cys2-16,com-cys7-16,com-as14-16,com-as31-16 ####################the four atoms involved in the torsional anglePBMETAD... # Carlo's Biasfactor rule-of-thumb: 10 * sqrt(number of CVs)Used to performed Parallel Bias metadynamics. More detailsBIASFACTOR=56use well tempered metadynamics with this bias factor, one for all biasesHEIGHT=0.3the height of the Gaussian hills, one for all biasesPACE=500000000the frequency for hill addition, one for all biasesWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRLABEL=pba label for the action so that its output can be referenced in the input to other actionsGRID_WSTRIDE=10000frequency for dumping the gridSIGMA=1000the widths of the Gaussian hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeARG=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7the input for this action is the scalar output from one or more other actionsSIGMA_MIN=0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.5,0.5,0.5,0.5,0.5,0.5,0.5the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,20,20,20,20,20,20,20the upper bounds for the sigmas (in CV units) when using adaptive hillsGRID_MIN=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0,0,0,0,0,0,0the lower bounds for the gridGRID_MAX=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,3820,3820,3820,3820,3820,3820,3820the upper bounds for the gridFILE=thomas_marco/HILLS_disulf1,thomas_marco/HILLS_disulf2,thomas_marco/HILLS_disulf3,thomas_marco/HILLS_disulf4,thomas_marco/HILLS_disulf5,thomas_marco/HILLS_disulf6,thomas_marco/HILLS_disulf7,thomas_marco/HILLS_disulf8,thomas_marco/HILLS_tor1,thomas_marco/HILLS_tor2,thomas_marco/HILLS_tor3,thomas_marco/HILLS_tor4,thomas_marco/HILLS_tor5,thomas_marco/HILLS_tor6,thomas_marco/HILLS_tor7,thomas_marco/HILLS_tor8,thomas_marco/HILLS_con1,thomas_marco/HILLS_con2,thomas_marco/HILLS_con3,thomas_marco/HILLS_con4,thomas_marco/HILLS_con5,thomas_marco/HILLS_con6,thomas_marco/HILLS_con7files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundGRID_RFILES=thomas_marco/GRID_disulf1,thomas_marco/GRID_disulf2,thomas_marco/GRID_disulf3,thomas_marco/GRID_disulf4,thomas_marco/GRID_disulf5,thomas_marco/GRID_disulf6,thomas_marco/GRID_disulf7,thomas_marco/GRID_disulf8,thomas_marco/GRID_tor1,thomas_marco/GRID_tor2,thomas_marco/GRID_tor3,thomas_marco/GRID_tor4,thomas_marco/GRID_tor5,thomas_marco/GRID_tor6,thomas_marco/GRID_tor7,thomas_marco/GRID_tor8,thomas_marco/GRID_con1,thomas_marco/GRID_con2,thomas_marco/GRID_con3,thomas_marco/GRID_con4,thomas_marco/GRID_con5,thomas_marco/GRID_con6,thomas_marco/GRID_con7read grid for the biasGRID_WFILES=thomas_marco/GRID_disulf1,thomas_marco/GRID_disulf2,thomas_marco/GRID_disulf3,thomas_marco/GRID_disulf4,thomas_marco/GRID_disulf5,thomas_marco/GRID_disulf6,thomas_marco/GRID_disulf7,thomas_marco/GRID_disulf8,thomas_marco/GRID_tor1,thomas_marco/GRID_tor2,thomas_marco/GRID_tor3,thomas_marco/GRID_tor4,thomas_marco/GRID_tor5,thomas_marco/GRID_tor6,thomas_marco/GRID_tor7,thomas_marco/GRID_tor8,thomas_marco/GRID_con1,thomas_marco/GRID_con2,thomas_marco/GRID_con3,thomas_marco/GRID_con4,thomas_marco/GRID_con5,thomas_marco/GRID_con6,thomas_marco/GRID_con7dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILESTEMP=310 ...the system temperature - this is only needed if you are doing well-tempered metadynamics
#EMMI ... # ARG=pb.bias REWEIGHT # LABEL=gmm NOPBC TEMP=310.0 NL_STRIDE=100 NL_CUTOFF=0.01 # ATOMS=protein-h GMM_FILE=../iapp.dat # # the larger the number the softer the contribution of the EM data # SIGMA0=5.0 SIGMA_MIN=0.05 DSIGMA=0.1 RESOLUTION=0.1 NOISETYPE=GAUSS # OPTSIGMAMEAN SIGMA_MEAN0=2.0 # AVERAGING=200 WRITE_STRIDE=10000 #...
# translate into bias #emr: BIASVALUE ARG=gmm.scoreb STRIDE=2
# print useful info to file #PRINT ARG=gmm.* FILE=EMMI STRIDE=500
#PRINT ARG=pb.bias FILE=FULLBIAS #PRINT ARG=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7,pb.bias FILE=COLVAR STRIDE=1 #PRINT ARG=disulf9,disulf10,disulf11,disulf12,disulf13,disulf14,disulf15,disulf16,tor9,tor10,tor11,tor12,tor13,tor14,tor15,tor16,con8,con9,con10,con11,con12,con13,con14 FILE=COLVAR_UNBIASED STRIDE=1Print quantities to a file. More detailsARG=disulf1,disulf2,disulf3,disulf4,disulf5,disulf6,disulf7,disulf8,tor1,tor2,tor3,tor4,tor5,tor6,tor7,tor8,con1,con2,con3,con4,con5,con6,con7,pb.bias,ph1,ph2,ph3,ph4,ph5,ph6,ph7,ph8,ph9,ph10,ph11,ph12,ph13,ph14,ph15,ph16,ph17,ph18,ph19,ph20,ph21,ph22,ph23,ph24,ps1,ps2,ps3,ps4,ps5,ps6,ps7,ps8,ps9,ps10,ps11,ps12,ps13,ps14,ps15,ps16,ps17,ps18,ps19,ps20,ps21,ps22,ps23,ps24the input for this action is the scalar output from one or more other actionsFILE=COLVAR_r3r4the name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output