Project ID: plumID:22.023
Source: ANALYSIS/plumed_analysis_unbiased.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
Click on the labels of the actions for more information on what each action computes
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#RESTARTMOLINFOThis 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
#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 tail2: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=tail2 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 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 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 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 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 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 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 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 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 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 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 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 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=tail15 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 anglePrint quantities to a file. More detailsARG=disulf9,disulf10,disulf11,disulf12,disulf13,disulf14,disulf15,disulf16,tor9,tor10,tor11,tor12,tor13,tor14,tor15,tor16,con8,con9,con10,con11,con12,con13,con14the input for this action is the scalar output from one or more other actionsFILE=COLVAR_UNBIASEDthe name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output