Project ID: plumID:20.033
Source: PRODUCTION/plumed.dat
Originally used with PLUMED version: 2.6
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
tested onv2.9
tested onmaster
#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
=structure.pdb
# define all heavy atoms using GROMACS index file

protein-h: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
protein: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein
Protein-noASPGLU-noH: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H_&_!GLU_ASP_&_OE1_OE2_OD1_OD2
system: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=System
# make protein whole: add reference position of first heavy atom (in nm)

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
=1-19086 
ENTITY1
the atoms that make up a molecule that you wish to align
=19087-38172 
ENTITY2
the atoms that make up a molecule that you wish to align
=38173-57258 
ADDREFERENCE
 Define the reference position of the first atom of each entity using a PDB file
 REF0=16.995,21.964,24.520 REF1=26.253,18.440,24.5030 REF2=24.616,28.069,24.203

RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=6vxx_1_1_1_aligned_struct_RBD_renumbered.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rmsd_closed_charmm_6vxx

RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd_structure_no487496.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rmsd_open

gly234NTFdown:  
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=3316,3318,3320,3323,3324,3325,3327,3328,17553,17555,17556,17558,17561,17563,17565,17567,17569,17571,17573,17574,17575,17579,17580,17582,17583,17585,17588,17590,17592,17594,17596,17598,17600,17601,17602,17606,17607,17609,17610,17612,17615,17616,17618,17620,17622,17624,17626,17627,17629,17631,17633,17635,17637,17640,17642,17643,17645,17647,17649,17651,17653,17655,17657,17659,17662,17664,17665,17667,17669 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=43296,43298,43300,43303,43304,43306,43308,43309,43311,43313,43315,43316,43317,43319,43321,43325,43326,44813,44815,44817,44820,44821,44822,44825,44826,44827,44829,44831,44834,44835,44837,44839,44840,44842,44844,44846,44847,44848,44850,44852,44855,44857,44861,44865,44866,44951,44953,44955,44958,44961,44964,44966,44967,44970,44973,44974,45041,45043,45045,45048,45051,45054,45057,45061,45062,45097,45099,45101,45104,45107,45108,45109,45110,45111,45112,45114,45116,45119,45122,45125,45127,45128,45131,45134,45135,45136,45138,45140,45143,45144,45145,45146,45147,45148,45150,45152,45154,45158,45161,45165,45166,45178,45180,45182,45184,45188,45190,45191,45192,45194,45196,45199,45202,45203,45204,45205,45206,45247,45249,45251,45254,45257,45258,45259,45262,45263 
LESS_THAN
calculate the number of variables less than a certain target value
={RATIONAL R_0=0.32 NN=6 MM=12}


gly165NTF_up:  
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=2196,2198,2200,2203,2204,2205,2207,2208,17435,17437,17438,17440,17443,17445,17447,17449,17451,17453,17455,17456,17457,17461,17462,17464,17465,17467,17470,17472,17474,17476,17478,17480,17482,17483,17484,17488,17489,17491,17492,17494,17497,17498,17500,17502,17504,17506,17508,17509,17511,17513,17515,17517,17519,17522,17524,17525,17527,17529,17531,17533,17535,17537,17539,17541,17544,17546,17547,17549,17551 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=43296,43298,43300,43303,43304,43306,43308,43309,43311,43313,43315,43316,43317,43319,43321,43325,43326,44813,44815,44817,44820,44821,44822,44825,44826,44827,44829,44831,44834,44835,44837,44839,44840,44842,44844,44846,44847,44848,44850,44852,44855,44857,44861,44865,44866,44951,44953,44955,44958,44961,44964,44966,44967,44970,44973,44974,45041,45043,45045,45048,45051,45054,45057,45061,45062,45097,45099,45101,45104,45107,45108,45109,45110,45111,45112,45114,45116,45119,45122,45125,45127,45128,45131,45134,45135,45136,45138,45140,45143,45144,45145,45146,45147,45148,45150,45152,45154,45158,45161,45165,45166,45178,45180,45182,45184,45188,45190,45191,45192,45194,45196,45199,45202,45203,45204,45205,45206,45247,45249,45251,45254,45257,45258,45259,45262,45263 
LESS_THAN
calculate the number of variables less than a certain target value
={RATIONAL R_0=0.32 NN=6 MM=12}

# create EMMI score

EMMI
Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=gmm 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
TEMP
temperature
=310.0 
NL_STRIDE
The frequency with which we are updating the neighbor list
=100 
NL_CUTOFF
The cutoff in overlap for the neighbor list
=0.01

ATOMS
atoms for which we calculate the density map, typically all heavy atoms
=Protein-noASPGLU-noH 
GMM_FILE
file with the parameters of the GMM components
=SARS_COV2.dat

SIGMA_MIN
minimum uncertainty
=0.05 
RESOLUTION
Cryo-EM map resolution
=0.1 
NOISETYPE
functional form of the noise (GAUSS, OUTLIERS, MARGINAL)
=MARGINAL
#WRITE_OV=OV_FILE.dat 
#WRITE_OV_STRIDE=500
...

# translate into bias
emr: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=gmm.scoreb 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2

# print useful info to file

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=5000