PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV7/plumed.6.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

#RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a 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 something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-709

RANDOM_EXCHANGES
Set random pattern for exchanges. More details

cv7The PARABETARMSD action with label cv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet: 
PARABETARMSD
Probe the parallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. More details
 
RESIDUES
this 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 
NN
 The n parameter of the switching function
=8 
MM
 The m parameter of the switching function
=12 
R_0
The r_0 parameter of the switching function
=0.08 
NOPBC
 ignore the periodic boundary conditions
cv7: 
PARABETARMSD
Probe the parallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. More details
 
RESIDUES
this 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 
NN
 The n parameter of the switching function
=8 
MM
 The m parameter of the switching function
=12 
R_0
The r_0 parameter of the switching function
=0.08 
NOPBC
 ignore the periodic boundary conditions
  
D_0
 The d_0 parameter of the switching function
=0.0 
STYLE
 Parallel beta sheets can either form in a single chain or from a pair of chains
=all
# PLUMED interprets the command:
# cv7: PARABETARMSD RESIDUES=1-45 TYPE=DRMSD NN=8 MM=12 R_0=0.08 NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
cv7_bothThe SECONDARY_STRUCTURE_RMSD action with label cv7_both calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7_both.struct-1
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 1th of these quantities
cv7_both.struct-2
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 2th of these quantities: 
SECONDARY_STRUCTURE_RMSD
Calclulate the distance between segments of a protein and a reference structure of interest More details
 
BONDLENGTH
the length to use for bonds
=0.17 
ATOMS
this 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
 
SEGMENT1
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 
SEGMENT2
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 
SEGMENT3
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 
SEGMENT4
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 
SEGMENT5
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64 
STRUCTURE1
the reference structure
=1.244,-4.62,-2.127,-0.016,-4.5,-1.395,0.105,-5.089,0.024,-0.287,-3,-1.301,0.55,-2.245,-0.822,-1.445,-2.551,-1.779,-1.752,-1.13,-1.677,-2.113,-0.55,-3.059,-2.906,-0.961,-0.689,-3.867,-1.738,-0.695,-2.774,0.034,0.19,-3.788,0.331,1.201,-3.188,0.3,2.624,-4.294,1.743,0.937,-3.503,2.671,0.821,4.746,-2.363,0.188,3.427,-1.839,0.545,3.135,-1.958,2.074,3.346,-0.365,0.181,4.237,0.412,0.521,2.261,0.013,-0.487,2.024,1.401,-0.875,1.489,1.514,-2.313,0.914,1.902,0.044,-0.173,1.33,0.052,1.202,2.94,0.828,0.19,3.507,1.718,0.772,3.801,3.104,-0.229,4.791,1.038,0.523,5.771,0.996 
STRUCTURE2
the reference structure
=-1.439,-5.122,-1.144,-0.816,-3.803,-1.013,0.099,-3.509,-2.206,-1.928,-2.77,-0.952,-2.991,-2.97,-1.551,-1.698,-1.687,-0.215,-2.681,-0.613,-0.143,-3.323,-0.477,1.267,-1.984,0.681,-0.574,-0.807,0.921,-0.273,-2.716,1.492,-1.329,-2.196,2.731,-1.883,-2.263,2.692,-3.418,-2.989,3.949,-1.433,-4.214,3.989,-1.583,2.464,-4.352,2.149,3.078,-3.17,1.541,3.398,-3.415,0.06,2.08,-2.021,1.639,0.938,-2.178,1.225,2.525,-0.886,2.183,1.692,0.303,2.346,1.541,0.665,3.842,2.42,1.41,1.608,3.567,1.733,1.937,1.758,1.976,0.6,2.373,2.987,-0.238,2.367,2.527,-1.72,1.684,4.331,-0.148,0.486,4.43,-0.415     # Action input conctinues with 698 further SEGMENTn keywords, 
cv7_lowThe LOWEST action with label cv7_low calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7_low
vector
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: 
LOWEST
This function can be used to find the lowest colvar by magnitude in a set. More details
 
ARG
the values input to this function
=cv7_both.struct-1,cv7_both.struct-2
cv7_ltThe LESS_THAN action with label cv7_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7_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_THAN
Use a switching function to determine how many of the input variables are less than a certain cutoff. More details
 
ARG
the values input to this function
=cv7_low 
SWITCH
This 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}
cv7The SUM action with label cv7 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv7
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=cv7_lt 
PERIODIC
if 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cv7 
AT
the positions of the wall
=0.0 
KAPPA
the 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_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cv7 
AT
the positions of the wall
=8.0 
KAPPA
the 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: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the labels of the scalars on which the bias will act
=cv7 
PACE
the frequency for hill addition
=2500 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=0.1 
FILE
 a file in which the list of added hills is stored
=HILLS 
GRID_MIN
the lower bounds for the grid
=0.0 
GRID_MAX
the upper bounds for the grid
=30.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.025

#PRINT STRIDE=10 ARG=cv7,metad.bias FILE=COLVAR
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the labels of the values that you would like to print to the file
=cv7,metad.bias,uwall.bias,lwall.bias 
FILE
the name of the file on which to output these quantities
=COLVAR