Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV5/plumed.4.dat
Originally used with PLUMED version: 2.5.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
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=Protein.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein
The MOLINFO action with label calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-709
RANDOM_EXCHANGESSet random pattern for exchanges. More details
cv5The ALPHARMSD action with label cv5 calculates the following quantities:| Quantity | Type | Description |
| cv5 | 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=1-45 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=2 MM The m parameter of the switching function=4 NOPBC ignore the periodic boundary conditions
cv5: 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=1-45 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=2 MM The m parameter of the switching function=4 NOPBC ignore the periodic boundary conditions D_0 The d_0 parameter of the switching function=0.0
# cv5: ALPHARMSD RESIDUES=1-45 TYPE=DRMSD R_0=0.08 NN=2 MM=4 NOPBC
cv5_rmsdThe SECONDARY_STRUCTURE_RMSD action with label cv5_rmsd calculates the following quantities:| Quantity | Type | Description |
| cv5_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=1,5,7,8,9,10,12,14,19,20,21,23,25,38,39,40,42,44,52,53,54,56,58,66,67,68,70,72,80,81,82,84,86,100,101,102,104,106,114,115,116,118,120,128,129,130,132,134,142,143,144,146,148,156,157,158,160,162,170,171,172,174,176,181,182,183,185,187,195,196,197,199,201,209,210,211,213,215,221,222,223,225,227,240,241,242,244,246,252,253,254,256,258,276,277,278,280,282,288,289,290,292,294,312,313,314,316,318,334,335,336,338,340,348,349,350,352,354,358,359,360,362,364,377,378,379,381,383,391,392,393,395,397,410,411,412,416,418,424,425,426,428,430,446,447,448,450,452,468,469,470,472,474,480,481,482,484,486,494,495,496,498,500,518,519,520,524,526,532,533,534,536,538,549,550,551,553,555,563,564,565,567,569,575,576,577,579,581,587,588,589,591,593,603,604,605,607,609,622,623,624,626,628,636,637,638,640,642,650,651,652,654,656,672,673,674,676,678,679,680,681,683,685,693,694 TYPE the manner in which RMSD alignment is performed=DRMSD NOPBC ignore the periodic boundary conditions 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
cv5_ltThe LESS_THAN action with label cv5_lt calculates the following quantities:| Quantity | Type | Description |
| cv5_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=cv5_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=2 MM=4}
cv5The SUM action with label cv5 calculates the following quantities:| Quantity | Type | Description |
| cv5 | 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=cv5_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv5 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=30.0
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Type | Description |
| uwall.bias | scalar | the instantaneous value of the bias potential |
| uwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv5 ATthe positions of the wall=15.0 KAPPAthe force constant for the wall=30.0
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=cv5 PACEthe frequency for hill addition=2500 HEIGHTthe heights of the Gaussian hills=0.3 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=30.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.025
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cv5,metad.bias,uwall.bias,lwall.bias FILEthe name of the file on which to output these quantities=COLVAR
