PLUMED-NEST

Project ID: plumID:22.000
Source: plumed-common-3.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=3.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details

hbondThe CONTACTMAP action with label hbond calculates the following quantities:
 Quantity   
 Type   
 Description  
hbond
scalar
the sum of all the switching function on all the distances: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=427,363 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT1A weight value for a given contact, by default is 1=0.09091 ATOMS2the atoms involved in each of the contacts you wish to calculate=405,346 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT2A weight value for a given contact, by default is 1=0.09091 ATOMS3the atoms involved in each of the contacts you wish to calculate=383,330 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT3A weight value for a given contact, by default is 1=0.09091 ATOMS4the atoms involved in each of the contacts you wish to calculate=364,311 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT4A weight value for a given contact, by default is 1=0.09091 ATOMS5the atoms involved in each of the contacts you wish to calculate=347,297 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT5A weight value for a given contact, by default is 1=0.09091 ATOMS6the atoms involved in each of the contacts you wish to calculate=331,278 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT6A weight value for a given contact, by default is 1=0.09091 ATOMS7the atoms involved in each of the contacts you wish to calculate=312,262 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT7A weight value for a given contact, by default is 1=0.09091 ATOMS8the atoms involved in each of the contacts you wish to calculate=298,243 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT8A weight value for a given contact, by default is 1=0.09091 ATOMS9the atoms involved in each of the contacts you wish to calculate=279,227 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT9A weight value for a given contact, by default is 1=0.09091 ATOMS10the atoms involved in each of the contacts you wish to calculate=263,213 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT10A weight value for a given contact, by default is 1=0.09091 ATOMS11the atoms involved in each of the contacts you wish to calculate=244,203 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.32} WEIGHT11A weight value for a given contact, by default is 1=0.09091 SUM calculate the sum of all the contacts in the input

alphaThe ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha
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=28-39 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 D_0 The d_0 parameter of the switching function=0.02
alpha: 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=28-39 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 D_0 The d_0 parameter of the switching function=0.02  NN The n parameter of the switching function=8 MM The m parameter of the switching function=12
# PLUMED interprets the command:
# alpha: ALPHARMSD RESIDUES=28-39 TYPE=OPTIMAL R_0=0.1 D_0=0.02
# as follows (Click the red comment above to revert to the short version of the input):
alpha_rmsdThe SECONDARY_STRUCTURE_RMSD action with label alpha_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_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=226,228,230,240,241,242,244,246,259,260,261,263,265,275,276,277,279,281,294,295,296,298,300,308,309,310,312,314,327,328,329,331,333,343,344,345,347,349,360,361,362,364,366,379,380,381,383,385,401,402,403,405,407,423,424,425,427,429,445,446 TYPE the manner in which RMSD alignment is performed=OPTIMAL 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     # Action input conctinues with 2 further SEGMENTn keywords, 
alpha_ltThe LESS_THAN action with label alpha_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha_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=alpha_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=0.02 NN=8 MM=12}
alphaThe SUM action with label alpha calculates the following quantities:
 Quantity   
 Type   
 Description  
alpha
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=alpha_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- app_headThe CENTER_FAST action with label app_head calculates the following quantities:
 Quantity   
 Type   
 Description  
app_head
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=230,246
app_tailThe CENTER_FAST action with label app_tail calculates the following quantities:
 Quantity   
 Type   
 Description  
app_tail
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=407,429
distanceThe DISTANCE action with label distance calculates the following quantities:
 Quantity   
 Type   
 Description  
distance
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=app_head,app_tail