PLUMED-NEST-TEST-SITE

Project ID: plumID:21.040
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

RESTARTActivate restart. More details

The RESTART 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=structure.pdb
# define all heavy atoms using GROMACS index file
# which can be created with gmx_mpi make_ndx
protein-h: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
The GROUP action with label protein-h calculates somethingprotein: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein
The GROUP action with label protein calculates somethingProtein-noASPGLU-noH: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=no_ASP_GLU_no_OE1_OE2_OD1_OD2_Protein-H
The GROUP action with label Protein-noASPGLU-noH calculates somethingsystem: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System
The GROUP action with label system calculates somethingbeta1: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=beta1
The GROUP action with label beta1 calculates somethingbeta2: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=beta2
The GROUP action with label beta2 calculates somethingbeta3: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=beta3
The GROUP action with label beta3 calculates somethingbeta4: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=beta4

The GROUP action with label beta4 calculates something50_48: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=50_48
The GROUP action with label 50_48 calculates something78_80: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=78_80
The GROUP action with label 78_80 calculates something109_111: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=109_111
The GROUP action with label 109_111 calculates something140_142: GROUPDefine 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_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=140_142

The GROUP action with label 140_142 calculates somethingbeta1_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=beta1
The COM action with label beta1_com calculates somethingbeta2_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=beta2
The COM action with label beta2_com calculates somethingbeta3_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=beta3
The COM action with label beta3_com calculates somethingbeta4_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=beta4

The COM action with label beta4_com calculates something50_48_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=50_48
The COM action with label 50_48_com calculates something78_80_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=78_80
The COM action with label 78_80_com calculates something109_111_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=109_111
The COM action with label 109_111_com calculates something140_142_com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=140_142

The COM action with label 140_142_com calculates somethingdistance1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta1_com,50_48_com
The DISTANCE action with label distance1 calculates the following quantities:
 Quantity   
 Description  
distance1.value
the DISTANCE between this pair of atomsdistance2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta2_com,78_80_com
The DISTANCE action with label distance2 calculates the following quantities:
 Quantity   
 Description  
distance2.value
the DISTANCE between this pair of atomsdistance3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta3_com,109_111_com
The DISTANCE action with label distance3 calculates the following quantities:
 Quantity   
 Description  
distance3.value
the DISTANCE between this pair of atomsdistance4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=beta4_com,140_142_com

#plus 1.3 
The DISTANCE action with label distance4 calculates the following quantities:
 Quantity   
 Description  
distance4.value
the DISTANCE between this pair of atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=distance1 ATthe positions of the wall=4.2 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall1
The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=distance2 ATthe positions of the wall=4.2 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall2
The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=distance3 ATthe positions of the wall=4.2 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall3
The UPPER_WALLS action with label uwall3 calculates the following quantities:
 Quantity   
 Description  
uwall3.bias
the instantaneous value of the bias potential
uwall3.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=distance4 ATthe positions of the wall=4.2 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall4

# make protein whole: add reference position of first heavy atom (in nm)
The UPPER_WALLS action with label uwall4 calculates the following quantities:
 Quantity   
 Description  
uwall4.bias
the instantaneous value of the bias potential
uwall4.force2
the instantaneous value of the squared force due to this bias potentialWHOLEMOLECULESThis 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=1-6840 ENTITY1the atoms that make up a molecule that you wish to align=6841-6880 ENTITY2the atoms that make up a molecule that you wish to align=6881-13814 ENTITY3the atoms that make up a molecule that you wish to align=13815-13859 ENTITY4the atoms that make up a molecule that you wish to align=13860-20699 ENTITY5the atoms that make up a molecule that you wish to align=20700-20739 ENTITY6the atoms that make up a molecule that you wish to align=20740-27673 ENTITY7the atoms that make up a molecule that you wish to align=27674-27718 ENTITY8the atoms that make up a molecule that you wish to align=27719-34558 ENTITY9the atoms that make up a molecule that you wish to align=34559-34598 ENTITY10the atoms that make up a molecule that you wish to align=34599-41532 ENTITY11the atoms that make up a molecule that you wish to align=41533-41577 ENTITY12the atoms that make up a molecule that you wish to align=41578-48417 ENTITY13the atoms that make up a molecule that you wish to align=48418-48457 ENTITY14the atoms that make up a molecule that you wish to align=48458-55391 ENTITY15the atoms that make up a molecule that you wish to align=55392-55436 ENTITY16the atoms that make up a molecule that you wish to align=55437-62276 ENTITY17the atoms that make up a molecule that you wish to align=62277-62316 ENTITY18the atoms that make up a molecule that you wish to align=62317-69250 ENTITY19the atoms that make up a molecule that you wish to align=69251-69295 ENTITY20the atoms that make up a molecule that you wish to align=69296-76135 ENTITY21the atoms that make up a molecule that you wish to align=76136-76175 ENTITY22the atoms that make up a molecule that you wish to align=76176-83109 ENTITY23the atoms that make up a molecule that you wish to align=83110-83154 ENTITY24the atoms that make up a molecule that you wish to align=83155-89994 ENTITY25the atoms that make up a molecule that you wish to align=89995-90034 ENTITY26the atoms that make up a molecule that you wish to align=90035-96968 ENTITY27the atoms that make up a molecule that you wish to align=96969-97013 ENTITY28the atoms that make up a molecule that you wish to align=97014-99997 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file REF0=34.307,44.84,8.469 REF1=35.495,45.583,5.476 REF2=34.303,44.744,12.551 REF3=35.512,45.661,9.382 REF4=34.387,44.82,16.569 REF5=35.575,45.562,13.575 REF6=34.384,44.724,20.65 REF7=35.593,45.641,17.481 REF8=34.468,44.799,24.668 REF9=35.656,45.542,21.675 REF10=34.464,44.703,28.75 REF11=35.673,45.621,25.581 REF12=34.549,44.779,32.768 REF13=35.737,45.521,29.774 REF14=34.545,44.683,36.849 REF15=35.754,45.6,33.68 REF16=34.63,44.758,40.868 REF17=35.818,45.501,37.874 REF18=34.626,44.663,44.949 REF19=35.835,45.58,41.78 REF20=34.71,44.738,48.967 REF21=35.898,45.48,45.973 REF22=34.707,44.642,53.049 REF23=35.915,45.559,49.88 REF24=34.791,44.717,57.067 REF25=35.979,45.46,54.073 REF26=34.787,44.622,61.148 REF27=35.996,45.539,57.979 REF28=37.207,50.967,0.94


# create EMMI score
EMMICalculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details ...
LABELa 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 TEMPtemperature=310.0 NL_STRIDEThe frequency with which we are updating the neighbor list=100 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01
ATOMSatoms for which we calculate the density map, typically all heavy atoms=Protein-noASPGLU-noH GMM_FILEfile with the parameters of the GMM components=MT_TAU.dat
#ATOMS selects what is refined
# no-negative-no-h or no-h are reasonable
# resolution is not used - no Bfactor fitting
# SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF,
# if crashes, raise back to 0.05,
# the larger the number the softer the contribution of the EM data
SIGMA_MINminimum uncertainty=0.03 RESOLUTIONCryo-EM map resolution=0.1 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=MARGINAL
#WRITE_OV=OV_FILE.dat 
#WRITE_OV_STRIDE=500
...
# translate into bias
The EMMI action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.acc
MC acceptance for uncertainty
gmm.sigma
uncertainty in the forward models and experiment
gmm.neff
effective number of replicasemr: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=gmm.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=2
#DUMPMASSCHARGE FILE=mcfile
# print useful info to file
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=5000