Project ID: plumID:19.005
Source: cmyc_and_10058_F4/plumed/plumed_master.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
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=../system/template.pdb
The MOLINFO action with label calculates somethingprotThe GROUP action with label prot calculates the following quantities: Quantity | Type | Description |
prot | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=1-191
drugThe GROUP action with label drug calculates the following quantities: Quantity | Type | Description |
drug | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=192-218
firstThe GROUP action with label first calculates the following quantities: Quantity | Type | Description |
first | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=1-76
secondThe GROUP action with label second calculates the following quantities: Quantity | Type | Description |
second | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=77-119
thirdThe GROUP action with label third calculates the following quantities: Quantity | Type | Description |
third | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=120-191
WHOLEMOLECULESThis 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=prot ENTITY1the atoms that make up a molecule that you wish to align=drug
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=meta_cv_plumed.dat
# INCLUDE FILE=meta_cv_plumed.dat
The INCLUDE action with label meta_cv_plumed.dat calculates somethingALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-403the four atoms that are required to calculate the phi dihedral for residue 403. Click here for more information. REFERENCE1the reference values for each of the torsional angles=-1.05
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-403the four atoms that are required to calculate the psi dihedral for residue 403. Click here for more information. REFERENCE2the reference values for each of the torsional angles=-0.79
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-404the four atoms that are required to calculate the phi dihedral for residue 404. Click here for more information. REFERENCE3the reference values for each of the torsional angles=-1.05
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-404the four atoms that are required to calculate the psi dihedral for residue 404. Click here for more information. REFERENCE4the reference values for each of the torsional angles=-0.79
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-405the four atoms that are required to calculate the phi dihedral for residue 405. Click here for more information. REFERENCE5the reference values for each of the torsional angles=-1.05
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-405the four atoms that are required to calculate the psi dihedral for residue 405. Click here for more information. REFERENCE6the reference values for each of the torsional angles=-0.79
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-406the four atoms that are required to calculate the phi dihedral for residue 406. Click here for more information. REFERENCE7the reference values for each of the torsional angles=-1.05
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-406the four atoms that are required to calculate the psi dihedral for residue 406. Click here for more information. REFERENCE8the reference values for each of the torsional angles=-0.79
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-407the four atoms that are required to calculate the phi dihedral for residue 407. Click here for more information. REFERENCE9the reference values for each of the torsional angles=-1.05
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-407the four atoms that are required to calculate the psi dihedral for residue 407. Click here for more information. REFERENCE10the reference values for each of the torsional angles=-0.79
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-408the four atoms that are required to calculate the phi dihedral for residue 408. Click here for more information. REFERENCE11the reference values for each of the torsional angles=-1.05
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-408the four atoms that are required to calculate the psi dihedral for residue 408. Click here for more information. REFERENCE12the reference values for each of the torsional angles=-0.79
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-409the four atoms that are required to calculate the phi dihedral for residue 409. Click here for more information. REFERENCE13the reference values for each of the torsional angles=-1.05
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-409the four atoms that are required to calculate the psi dihedral for residue 409. Click here for more information. REFERENCE14the reference values for each of the torsional angles=-0.79
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-410the four atoms that are required to calculate the phi dihedral for residue 410. Click here for more information. REFERENCE15the reference values for each of the torsional angles=-1.05
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-410the four atoms that are required to calculate the psi dihedral for residue 410. Click here for more information. REFERENCE16the reference values for each of the torsional angles=-0.79
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-411the four atoms that are required to calculate the phi dihedral for residue 411. Click here for more information. REFERENCE17the reference values for each of the torsional angles=-1.05
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-411the four atoms that are required to calculate the psi dihedral for residue 411. Click here for more information. REFERENCE18the reference values for each of the torsional angles=-0.79
LABELa label for the action so that its output can be referenced in the input to other actions=ahelixrightThe SUM action with label ahelixright calculates the following quantities: Quantity | Type | Description |
ahelixright | scalar | the sum of all the elements in the input vector |
... ALPHABETA
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-403the four atoms that are required to calculate the phi dihedral for residue 403. Click here for more information. REFERENCE1the reference values for each of the torsional angles=-2.36
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-403the four atoms that are required to calculate the psi dihedral for residue 403. Click here for more information. REFERENCE2the reference values for each of the torsional angles=2.36
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-404the four atoms that are required to calculate the phi dihedral for residue 404. Click here for more information. REFERENCE3the reference values for each of the torsional angles=-2.36
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-404the four atoms that are required to calculate the psi dihedral for residue 404. Click here for more information. REFERENCE4the reference values for each of the torsional angles=2.36
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-405the four atoms that are required to calculate the phi dihedral for residue 405. Click here for more information. REFERENCE5the reference values for each of the torsional angles=-2.36
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-405the four atoms that are required to calculate the psi dihedral for residue 405. Click here for more information. REFERENCE6the reference values for each of the torsional angles=2.36
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-406the four atoms that are required to calculate the phi dihedral for residue 406. Click here for more information. REFERENCE7the reference values for each of the torsional angles=-2.36
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-406the four atoms that are required to calculate the psi dihedral for residue 406. Click here for more information. REFERENCE8the reference values for each of the torsional angles=2.36
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-407the four atoms that are required to calculate the phi dihedral for residue 407. Click here for more information. REFERENCE9the reference values for each of the torsional angles=-2.36
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-407the four atoms that are required to calculate the psi dihedral for residue 407. Click here for more information. REFERENCE10the reference values for each of the torsional angles=2.36
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-408the four atoms that are required to calculate the phi dihedral for residue 408. Click here for more information. REFERENCE11the reference values for each of the torsional angles=-2.36
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-408the four atoms that are required to calculate the psi dihedral for residue 408. Click here for more information. REFERENCE12the reference values for each of the torsional angles=2.36
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-409the four atoms that are required to calculate the phi dihedral for residue 409. Click here for more information. REFERENCE13the reference values for each of the torsional angles=-2.36
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-409the four atoms that are required to calculate the psi dihedral for residue 409. Click here for more information. REFERENCE14the reference values for each of the torsional angles=2.36
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-410the four atoms that are required to calculate the phi dihedral for residue 410. Click here for more information. REFERENCE15the reference values for each of the torsional angles=-2.36
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-410the four atoms that are required to calculate the psi dihedral for residue 410. Click here for more information. REFERENCE16the reference values for each of the torsional angles=2.36
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-411the four atoms that are required to calculate the phi dihedral for residue 411. Click here for more information. REFERENCE17the reference values for each of the torsional angles=-2.36
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-411the four atoms that are required to calculate the psi dihedral for residue 411. Click here for more information. REFERENCE18the reference values for each of the torsional angles=2.36
LABELa label for the action so that its output can be referenced in the input to other actions=betasheetThe SUM action with label betasheet calculates the following quantities: Quantity | Type | Description |
betasheet | scalar | the sum of all the elements in the input vector |
... ALPHABETA
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-403the four atoms that are required to calculate the phi dihedral for residue 403. Click here for more information. REFERENCE1the reference values for each of the torsional angles=1.05
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-403the four atoms that are required to calculate the psi dihedral for residue 403. Click here for more information. REFERENCE2the reference values for each of the torsional angles=1.05
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-404the four atoms that are required to calculate the phi dihedral for residue 404. Click here for more information. REFERENCE3the reference values for each of the torsional angles=1.05
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-404the four atoms that are required to calculate the psi dihedral for residue 404. Click here for more information. REFERENCE4the reference values for each of the torsional angles=1.05
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-405the four atoms that are required to calculate the phi dihedral for residue 405. Click here for more information. REFERENCE5the reference values for each of the torsional angles=1.05
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-405the four atoms that are required to calculate the psi dihedral for residue 405. Click here for more information. REFERENCE6the reference values for each of the torsional angles=1.05
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-406the four atoms that are required to calculate the phi dihedral for residue 406. Click here for more information. REFERENCE7the reference values for each of the torsional angles=1.05
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-406the four atoms that are required to calculate the psi dihedral for residue 406. Click here for more information. REFERENCE8the reference values for each of the torsional angles=1.05
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-407the four atoms that are required to calculate the phi dihedral for residue 407. Click here for more information. REFERENCE9the reference values for each of the torsional angles=1.05
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-407the four atoms that are required to calculate the psi dihedral for residue 407. Click here for more information. REFERENCE10the reference values for each of the torsional angles=1.05
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-408the four atoms that are required to calculate the phi dihedral for residue 408. Click here for more information. REFERENCE11the reference values for each of the torsional angles=1.05
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-408the four atoms that are required to calculate the psi dihedral for residue 408. Click here for more information. REFERENCE12the reference values for each of the torsional angles=1.05
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-409the four atoms that are required to calculate the phi dihedral for residue 409. Click here for more information. REFERENCE13the reference values for each of the torsional angles=1.05
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-409the four atoms that are required to calculate the psi dihedral for residue 409. Click here for more information. REFERENCE14the reference values for each of the torsional angles=1.05
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-410the four atoms that are required to calculate the phi dihedral for residue 410. Click here for more information. REFERENCE15the reference values for each of the torsional angles=1.05
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-410the four atoms that are required to calculate the psi dihedral for residue 410. Click here for more information. REFERENCE16the reference values for each of the torsional angles=1.05
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-411the four atoms that are required to calculate the phi dihedral for residue 411. Click here for more information. REFERENCE17the reference values for each of the torsional angles=1.05
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-411the four atoms that are required to calculate the psi dihedral for residue 411. Click here for more information. REFERENCE18the reference values for each of the torsional angles=1.05
LABELa label for the action so that its output can be referenced in the input to other actions=ahelixleftThe SUM action with label ahelixleft calculates the following quantities: Quantity | Type | Description |
ahelixleft | scalar | the sum of all the elements in the input vector |
... ALPHABETA
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-403the four atoms that are required to calculate the phi dihedral for residue 403. Click here for more information. REFERENCE1the reference values for each of the torsional angles=-1.31
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-403the four atoms that are required to calculate the psi dihedral for residue 403. Click here for more information. REFERENCE2the reference values for each of the torsional angles=2.71
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-404the four atoms that are required to calculate the phi dihedral for residue 404. Click here for more information. REFERENCE3the reference values for each of the torsional angles=-1.31
ATOMS4the atoms involved for each of the torsions you wish to calculate=@psi-404the four atoms that are required to calculate the psi dihedral for residue 404. Click here for more information. REFERENCE4the reference values for each of the torsional angles=2.71
ATOMS5the atoms involved for each of the torsions you wish to calculate=@phi-405the four atoms that are required to calculate the phi dihedral for residue 405. Click here for more information. REFERENCE5the reference values for each of the torsional angles=-1.31
ATOMS6the atoms involved for each of the torsions you wish to calculate=@psi-405the four atoms that are required to calculate the psi dihedral for residue 405. Click here for more information. REFERENCE6the reference values for each of the torsional angles=2.71
ATOMS7the atoms involved for each of the torsions you wish to calculate=@phi-406the four atoms that are required to calculate the phi dihedral for residue 406. Click here for more information. REFERENCE7the reference values for each of the torsional angles=-1.31
ATOMS8the atoms involved for each of the torsions you wish to calculate=@psi-406the four atoms that are required to calculate the psi dihedral for residue 406. Click here for more information. REFERENCE8the reference values for each of the torsional angles=2.71
ATOMS9the atoms involved for each of the torsions you wish to calculate=@phi-407the four atoms that are required to calculate the phi dihedral for residue 407. Click here for more information. REFERENCE9the reference values for each of the torsional angles=-1.31
ATOMS10the atoms involved for each of the torsions you wish to calculate=@psi-407the four atoms that are required to calculate the psi dihedral for residue 407. Click here for more information. REFERENCE10the reference values for each of the torsional angles=2.71
ATOMS11the atoms involved for each of the torsions you wish to calculate=@phi-408the four atoms that are required to calculate the phi dihedral for residue 408. Click here for more information. REFERENCE11the reference values for each of the torsional angles=-1.31
ATOMS12the atoms involved for each of the torsions you wish to calculate=@psi-408the four atoms that are required to calculate the psi dihedral for residue 408. Click here for more information. REFERENCE12the reference values for each of the torsional angles=2.71
ATOMS13the atoms involved for each of the torsions you wish to calculate=@phi-409the four atoms that are required to calculate the phi dihedral for residue 409. Click here for more information. REFERENCE13the reference values for each of the torsional angles=-1.31
ATOMS14the atoms involved for each of the torsions you wish to calculate=@psi-409the four atoms that are required to calculate the psi dihedral for residue 409. Click here for more information. REFERENCE14the reference values for each of the torsional angles=2.71
ATOMS15the atoms involved for each of the torsions you wish to calculate=@phi-410the four atoms that are required to calculate the phi dihedral for residue 410. Click here for more information. REFERENCE15the reference values for each of the torsional angles=-1.31
ATOMS16the atoms involved for each of the torsions you wish to calculate=@psi-410the four atoms that are required to calculate the psi dihedral for residue 410. Click here for more information. REFERENCE16the reference values for each of the torsional angles=2.71
ATOMS17the atoms involved for each of the torsions you wish to calculate=@phi-411the four atoms that are required to calculate the phi dihedral for residue 411. Click here for more information. REFERENCE17the reference values for each of the torsional angles=-1.31
ATOMS18the atoms involved for each of the torsions you wish to calculate=@psi-411the four atoms that are required to calculate the psi dihedral for residue 411. Click here for more information. REFERENCE18the reference values for each of the torsional angles=2.71
LABELa label for the action so that its output can be referenced in the input to other actions=polyproThe SUM action with label polypro calculates the following quantities: Quantity | Type | Description |
polypro | scalar | the sum of all the elements in the input vector |
... ALPHABETA
caThe GROUP action with label ca calculates the following quantities: Quantity | Type | Description |
ca | atoms | indices of atoms specified in GROUP |
: 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 ATOMSthe numerical indexes for the set of atoms in the group=9,30,49,68,79,95,112,122,137,152,169
rgyrThe GYRATION action with label rgyr calculates the following quantities: Quantity | Type | Description |
rgyr | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=ca
ohbondThe COORDINATION action with label ohbond calculates the following quantities: Quantity | Type | Description |
ohbond | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6,27,46,65,76,92,109,119,134,149,166,188 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=8,29,48,67,78,94,111,121,136,151,168 D_0 The d_0 parameter of the switching function=0 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=drug LABELa label for the action so that its output can be referenced in the input to other actions=drThe CENTER_FAST action with label dr calculates the following quantities: Quantity | Type | Description |
dr | 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=first LABELa label for the action so that its output can be referenced in the input to other actions=fstThe CENTER_FAST action with label fst calculates the following quantities: Quantity | Type | Description |
fst | 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=second LABELa label for the action so that its output can be referenced in the input to other actions=scdThe CENTER_FAST action with label scd calculates the following quantities: Quantity | Type | Description |
scd | 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=third LABELa label for the action so that its output can be referenced in the input to other actions=trdThe CENTER_FAST action with label trd calculates the following quantities: Quantity | Type | Description |
trd | atoms | virtual atom calculated by CENTER_FAST action |
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=fst,dr LABELa label for the action so that its output can be referenced in the input to other actions=fstdrThe DISTANCE action with label fstdr calculates the following quantities: Quantity | Type | Description |
fstdr | 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=scd,dr LABELa label for the action so that its output can be referenced in the input to other actions=scddrThe DISTANCE action with label scddr calculates the following quantities: Quantity | Type | Description |
scddr | 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=trd,dr LABELa label for the action so that its output can be referenced in the input to other actions=trddrThe DISTANCE action with label trddr calculates the following quantities: Quantity | Type | Description |
trddr | scalar | the DISTANCE between this pair of atoms |
# --- End of included input ---
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=pbmetadThe PBMETAD action with label pbmetad calculates the following quantities: Quantity | Type | Description |
pbmetad.bias | scalar | the instantaneous value of the bias potential |
ARGthe labels of the scalars on which the bias will act=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,fstdr,scddr,trddr
PACEthe frequency for hill addition, one for all biases=500 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=10 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
SIGMAthe widths of the Gaussian hills=1.01,0.89,0.41,0.72,0.05,0.71,0.05,0.05,0.05
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_ahelixright,HILLS_betasheet,HILLS_ahelixleft,HILLS_polypro,HILLS_rgyr,HILLS_ohbond,HILLS_fstdr,HILLS_scddr,HILLS_trddr
GRID_MINthe lower bounds for the grid=-2,-2,-2,-2,0.2,0,0,0,0
GRID_MAXthe upper bounds for the grid=20,20,20,20,1.4,30,5.2,5.2,5.2
... PBMETAD
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=exp_cv_plumed.dat
# INCLUDE FILE=exp_cv_plumed.dat
The INCLUDE action with label exp_cv_plumed.dat calculates somethingcsThe CS2BACKBONE action with label cs calculates the following quantities: Quantity | Type | Description |
cs.ca-0-403 | scalar | the calculated Ca carbon chemical shifts This is the 0-403th of these quantities |
cs.ca-0-404 | scalar | the calculated Ca carbon chemical shifts This is the 0-404th of these quantities |
cs.ca-0-405 | scalar | the calculated Ca carbon chemical shifts This is the 0-405th of these quantities |
cs.ca-0-406 | scalar | the calculated Ca carbon chemical shifts This is the 0-406th of these quantities |
cs.ca-0-407 | scalar | the calculated Ca carbon chemical shifts This is the 0-407th of these quantities |
cs.ca-0-408 | scalar | the calculated Ca carbon chemical shifts This is the 0-408th of these quantities |
cs.ca-0-409 | scalar | the calculated Ca carbon chemical shifts This is the 0-409th of these quantities |
cs.ca-0-410 | scalar | the calculated Ca carbon chemical shifts This is the 0-410th of these quantities |
cs.ca-0-411 | scalar | the calculated Ca carbon chemical shifts This is the 0-411th of these quantities |
cs.cb-0-404 | scalar | the calculated Cb carbon chemical shifts This is the 0-404th of these quantities |
cs.cb-0-405 | scalar | the calculated Cb carbon chemical shifts This is the 0-405th of these quantities |
cs.cb-0-408 | scalar | the calculated Cb carbon chemical shifts This is the 0-408th of these quantities |
cs.ha-0-403 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-403th of these quantities |
cs.ha-0-404 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-404th of these quantities |
cs.ha-0-405 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-405th of these quantities |
cs.ha-0-406 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-406th of these quantities |
cs.ha-0-407 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-407th of these quantities |
cs.ha-0-408 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-408th of these quantities |
cs.ha-0-409 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-409th of these quantities |
cs.ha-0-410 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-410th of these quantities |
cs.ha-0-411 | scalar | the calculated Ha hydrogen chemical shifts This is the 0-411th of these quantities |
cs.expca-0-403 | scalar | the experimental Ca carbon chemical shifts This is the 0-403th of these quantities |
cs.expca-0-404 | scalar | the experimental Ca carbon chemical shifts This is the 0-404th of these quantities |
cs.expca-0-405 | scalar | the experimental Ca carbon chemical shifts This is the 0-405th of these quantities |
cs.expca-0-406 | scalar | the experimental Ca carbon chemical shifts This is the 0-406th of these quantities |
cs.expca-0-407 | scalar | the experimental Ca carbon chemical shifts This is the 0-407th of these quantities |
cs.expca-0-408 | scalar | the experimental Ca carbon chemical shifts This is the 0-408th of these quantities |
cs.expca-0-409 | scalar | the experimental Ca carbon chemical shifts This is the 0-409th of these quantities |
cs.expca-0-410 | scalar | the experimental Ca carbon chemical shifts This is the 0-410th of these quantities |
cs.expca-0-411 | scalar | the experimental Ca carbon chemical shifts This is the 0-411th of these quantities |
cs.expcb-0-404 | scalar | the experimental Cb carbon chemical shifts This is the 0-404th of these quantities |
cs.expcb-0-405 | scalar | the experimental Cb carbon chemical shifts This is the 0-405th of these quantities |
cs.expcb-0-408 | scalar | the experimental Cb carbon chemical shifts This is the 0-408th of these quantities |
cs.expha-0-403 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-403th of these quantities |
cs.expha-0-404 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-404th of these quantities |
cs.expha-0-405 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-405th of these quantities |
cs.expha-0-406 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-406th of these quantities |
cs.expha-0-407 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-407th of these quantities |
cs.expha-0-408 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-408th of these quantities |
cs.expha-0-409 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-409th of these quantities |
cs.expha-0-410 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-410th of these quantities |
cs.expha-0-411 | scalar | the experimental Ha hydrogen chemical shifts This is the 0-411th of these quantities |
: CS2BACKBONECalculates the backbone chemical shifts for a protein. More details ATOMSThe atoms to be included in the calculation, e=7-188 TEMPLATE A PDB file of the protein system=../system/template.pdb DATADIR The folder with the experimental chemical shifts=../data NOPBC ignore the periodic boundary conditions when calculating distances
# --- End of included input ---
mi_cs_haThe METAINFERENCE action with label mi_cs_ha calculates the following quantities: Quantity | Type | Description |
mi_cs_ha.bias | scalar | the instantaneous value of the bias potential |
mi_cs_ha.biasDer | scalar | derivatives with respect to the bias |
mi_cs_ha.weight | scalar | weights of the weighted average |
mi_cs_ha.neff | scalar | effective number of replicas |
mi_cs_ha.acceptSigma | scalar | MC acceptance for sigma values |
mi_cs_ha.sigmaMean | scalar | uncertainty in the mean estimate |
mi_cs_ha.sigma | scalar | uncertainty parameter |
: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=(cs\.ha-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expha-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_ha: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=(cs\.ha-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expha-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE
mi_cs_caThe METAINFERENCE action with label mi_cs_ca calculates the following quantities: Quantity | Type | Description |
mi_cs_ca.bias | scalar | the instantaneous value of the bias potential |
mi_cs_ca.biasDer | scalar | derivatives with respect to the bias |
mi_cs_ca.weight | scalar | weights of the weighted average |
mi_cs_ca.neff | scalar | effective number of replicas |
mi_cs_ca.acceptSigma | scalar | MC acceptance for sigma values |
mi_cs_ca.sigmaMean | scalar | uncertainty in the mean estimate |
mi_cs_ca.sigma | scalar | uncertainty parameter |
: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=(cs\.ca-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expca-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_ca: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=(cs\.ca-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expca-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE
mi_cs_cbThe METAINFERENCE action with label mi_cs_cb calculates the following quantities: Quantity | Type | Description |
mi_cs_cb.bias | scalar | the instantaneous value of the bias potential |
mi_cs_cb.biasDer | scalar | derivatives with respect to the bias |
mi_cs_cb.weight | scalar | weights of the weighted average |
mi_cs_cb.neff | scalar | effective number of replicas |
mi_cs_cb.acceptSigma | scalar | MC acceptance for sigma values |
mi_cs_cb.sigmaMean | scalar | uncertainty in the mean estimate |
mi_cs_cb.sigma | scalar | uncertainty parameter |
: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=(cs\.cb-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expcb-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_cb: METAINFERENCECalculates the Metainference energy for a set of experimental data. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=(cs\.cb-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expcb-.*) REWEIGHT simple REWEIGHT using the latest ARG as energy NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS SIGMA0 initial value of the uncertainty parameter=1.0 SIGMA_MIN minimum value of the uncertainty parameter=0.00001 SIGMA_MAX maximum value of the uncertainty parameter=10.0 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=10000 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=NONE
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,fstdr,scddr,trddr,pbmetad.bias FILEthe name of the file on which to output these quantities=COLVAR_PBMETAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=mi_cs_ha.*,mi_cs_ca.*,mi_cs_cb.* FILEthe name of the file on which to output these quantities=COLVAR_MI