Project ID: plumID:22.000
Source: plumed-common-2.dat
Originally used with PLUMED version: 2.5
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=nm TIMEthe units of time=ps ENERGYthe units of energy=kj/mol
The UNITS action with label calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=2.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details
ab48The COORDINATION action with label ab48 calculates the following quantities:| Quantity | Type | Description |
| ab48 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5452,5453,5454,5455 R_0The r_0 parameter of the switching function=0.45
ab48: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5452,5453,5454,5455 R_0The r_0 parameter of the switching function=0.45 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
ab49The COORDINATION action with label ab49 calculates the following quantities:| Quantity | Type | Description |
| ab49 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5471,5472,5473,5474 R_0The r_0 parameter of the switching function=0.45
ab49: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5471,5472,5473,5474 R_0The r_0 parameter of the switching function=0.45 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
ab50The COORDINATION action with label ab50 calculates the following quantities:| Quantity | Type | Description |
| ab50 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5487,5488,5489,5490 R_0The r_0 parameter of the switching function=0.45
ab50: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5487,5488,5489,5490 R_0The r_0 parameter of the switching function=0.45 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
anti1The ANTIBETARMSD action with label anti1 calculates the following quantities:| Quantity | Type | Description |
| anti1 | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
anti1: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12
# anti1: ANTIBETARMSD RESIDUES=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1 STYLE=inter
anti1_rmsdThe SECONDARY_STRUCTURE_RMSD action with label anti1_rmsd calculates the following quantities:| Quantity | Type | Description |
| anti1_rmsd | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=3700,3702,3704,3722,3723,3724,3726,3728,3729,3730,3731,3733,3735,3745,3746,3747,3749,3751,3767,3768,3769,3771,3773,3786,3787,3788,3790,3792,3793,3794,3795,3797,3799,3812,3813,3814,3816,3818,3819,3820,5439,5441,5443,5451,5452,5453,5455,5457,5470,5471,5472,5474,5476,5486,5487,5488,5490,5492,5503,5504,5505,5507,5509,5522,5523,5524,5526,5528,5544,5545,5546,5548,5550,5566,5567 TYPE the manner in which RMSD alignment is performed=OPTIMAL STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 SEGMENT1this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14 SEGMENT2this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19 SEGMENT3this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 SEGMENT4this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT5this is the lists of atoms in the segment that are being considered=40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102
anti1_ltThe LESS_THAN action with label anti1_lt calculates the following quantities:| Quantity | Type | Description |
| anti1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=anti1_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12}
anti1The SUM action with label anti1 calculates the following quantities:| Quantity | Type | Description |
| anti1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=anti1_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- anti2The ANTIBETARMSD action with label anti2 calculates the following quantities:| Quantity | Type | Description |
| anti2 | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=430,431,432,433,434,435,32,33,34,35,36,37 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
anti2: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=430,431,432,433,434,435,32,33,34,35,36,37 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12
# anti2: ANTIBETARMSD RESIDUES=430,431,432,433,434,435,32,33,34,35,36,37 TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1 STYLE=inter
anti2_rmsdThe SECONDARY_STRUCTURE_RMSD action with label anti2_rmsd calculates the following quantities:| Quantity | Type | Description |
| anti2_rmsd | vector | a vector containing the rmsd distance between each of the residue segments and the reference structure |
: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=4515,4517,4519,4535,4536,4537,4539,4541,4545,4546,4547,4549,4551,4564,4565,4566,4570,4572,4578,4579,4580,4582,4584,4588,4589,4590,4592,4594,4607,4608,5439,5441,5443,5451,5452,5453,5455,5457,5470,5471,5472,5474,5476,5486,5487,5488,5490,5492,5503,5504,5505,5507,5509,5522,5523,5524,5526,5528,5544,5545 TYPE the manner in which RMSD alignment is performed=OPTIMAL STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 SEGMENT1this is the lists of atoms in the segment that are being considered=30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14 SEGMENT2this is the lists of atoms in the segment that are being considered=30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19 SEGMENT3this is the lists of atoms in the segment that are being considered=30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 SEGMENT4this is the lists of atoms in the segment that are being considered=30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT5this is the lists of atoms in the segment that are being considered=35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102
anti2_ltThe LESS_THAN action with label anti2_lt calculates the following quantities:| Quantity | Type | Description |
| anti2_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=anti2_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12}
anti2The SUM action with label anti2 calculates the following quantities:| Quantity | Type | Description |
| anti2 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=anti2_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
cat_siteThe CENTER_FAST action with label cat_site calculates the following quantities:| Quantity | Type | Description |
| cat_site | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=3043,3824
ab48_siteThe CENTER_FAST action with label ab48_site calculates the following quantities:| Quantity | Type | Description |
| ab48_site | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5442,5456
ab49_siteThe CENTER_FAST action with label ab49_site calculates the following quantities:| Quantity | Type | Description |
| ab49_site | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5456,5475
ab50_siteThe CENTER_FAST action with label ab50_site calculates the following quantities:| Quantity | Type | Description |
| ab50_site | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5475,5491
dis_ab48The DISTANCE action with label dis_ab48 calculates the following quantities:| Quantity | Type | Description |
| dis_ab48 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab48_site
dis_ab49The DISTANCE action with label dis_ab49 calculates the following quantities:| Quantity | Type | Description |
| dis_ab49 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab49_site
dis_ab50The DISTANCE action with label dis_ab50 calculates the following quantities:| Quantity | Type | Description |
| dis_ab50 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab50_site
