Project ID: plumID:19.020
Source: step-2/plumed.4.dat
Originally used with PLUMED version: 2.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
MOLINFOThis 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=reference.pdb
The MOLINFO action with label calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-427
aThe ALPHARMSD action with label a calculates the following quantities:| Quantity | Type | Description |
| a | scalar | if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix. If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix |
: ALPHARMSDProbe the alpha helical content of a 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=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12
a: ALPHARMSDProbe the alpha helical content of a 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=all TYPE the manner in which RMSD alignment is performed=DRMSD R_0The r_0 parameter of the switching function=0.08 NN The n parameter of the switching function=8 MM The m parameter of the switching function=12 D_0 The d_0 parameter of the switching function=0.0
# a: ALPHARMSD RESIDUES=all TYPE=DRMSD R_0=0.08 NN=8 MM=12
a_rmsdThe SECONDARY_STRUCTURE_RMSD action with label a_rmsd calculates the following quantities:| Quantity | Type | Description |
| a_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=7,9,11,19,20,21,23,25,31,32,33,35,37,46,47,48,50,52,58,59,60,62,64,74,75,76,78,80,85,86,87,89,91,97,98,99,101,103,116,117,118,120,122,131,132,133,135,137,155,156,157,159,161,179,180,181,183,185,198,199,200,202,204,208,209,210,212,214,225,226,227,229,231,249,250,251,253,255,268,269,270,272,274,278,279,280,282,284,293,294,295,297,299,317,318,319,321,323,341,342,343,345,347,358,359,360,362,364,373,374,375,377,379,385,386,387,389,391,396,397,398,400,402,406,407,408,410,412,420,421 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673
a_ltThe LESS_THAN action with label a_lt calculates the following quantities:| Quantity | Type | Description |
| a_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=a_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
aThe SUM action with label a calculates the following quantities:| Quantity | Type | Description |
| a | 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=a_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- gThe GYRATION action with label g calculates the following quantities:| Quantity | Type | Description |
| g | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=9,23,35,50,62,78,89,101,120,135,159,183,202,212,229,253,272,282,297,321,345,362,377,389,400,410
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
wteThe METAD action with label wte calculates the following quantities:| Quantity | Type | Description |
| wte.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ene PACEthe frequency for hill addition=999999999 HEIGHTthe heights of the Gaussian hills=2.5 SIGMAthe widths of the Gaussian hills=500.0 FILE a file in which the list of added hills is stored=HILLS_PTWTE BIASFACTORuse well tempered metadynamics and use this bias factor=50.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=352.59
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=a,g PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=0.4184 SIGMAthe widths of the Gaussian hills=0.15,0.025 FILE a file in which the list of added hills is stored=HILLS_PTMetaDWTE BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=352.59
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a,g,ene,wte.bias,metad.bias STRIDE the frequency with which the quantities of interest should be output=50 FILEthe name of the file on which to output these quantities=COLVAR_MetadWTE
ENDPLUMEDTerminate plumed input. More details
