Project ID: plumID:22.000
Source: plumed-2.0.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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-common-2.dat
# INCLUDE FILE=plumed-common-2.dat
The INCLUDE action with label plumed-common-2.dat calculates somethingUNITSThis 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=2.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details
ab48The COORDINATION action with label ab48 calculates the following quantities:| Quantity | Type | Description |
| ab48 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5452,5453,5454,5455 R_0The r_0 parameter of the switching function=0.45
ab49The COORDINATION action with label ab49 calculates the following quantities:| Quantity | Type | Description |
| ab49 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5471,5472,5473,5474 R_0The r_0 parameter of the switching function=0.45
ab50The COORDINATION action with label ab50 calculates the following quantities:| Quantity | Type | Description |
| ab50 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5487,5488,5489,5490 R_0The r_0 parameter of the switching function=0.45
anti1The SUM action with label anti1 calculates the following quantities:| Quantity | Type | Description |
| anti1 | scalar | the sum of all the elements in the input vector |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
anti2The SUM action with label anti2 calculates the following quantities:| Quantity | Type | Description |
| anti2 | scalar | the sum of all the elements in the input vector |
: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=430,431,432,433,434,435,32,33,34,35,36,37 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
cat_siteThe CENTER_FAST action with label cat_site calculates the following quantities:| Quantity | Type | Description |
| cat_site | 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=3043,3824
ab48_siteThe CENTER_FAST action with label ab48_site calculates the following quantities:| Quantity | Type | Description |
| ab48_site | 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=5442,5456
ab49_siteThe CENTER_FAST action with label ab49_site calculates the following quantities:| Quantity | Type | Description |
| ab49_site | 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=5456,5475
ab50_siteThe CENTER_FAST action with label ab50_site calculates the following quantities:| Quantity | Type | Description |
| ab50_site | 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=5475,5491
dis_ab48The DISTANCE action with label dis_ab48 calculates the following quantities:| Quantity | Type | Description |
| dis_ab48 | 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=cat_site,ab48_site
dis_ab49The DISTANCE action with label dis_ab49 calculates the following quantities:| Quantity | Type | Description |
| dis_ab49 | 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=cat_site,ab49_site
dis_ab50The DISTANCE action with label dis_ab50 calculates the following quantities:| Quantity | Type | Description |
| dis_ab50 | 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=cat_site,ab50_site
# --- End of included input ---
be0The METAD action with label be0 calculates the following quantities:| Quantity | Type | Description |
| be0.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ab48 SIGMAthe widths of the Gaussian hills=1 HEIGHTthe heights of the Gaussian hills=1.0 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 PACEthe frequency for hill addition=2000 FILE a file in which the list of added hills is stored=HILLS GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.5 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=30
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab48,ab49,dis_ab48,dis_ab49,anti1,anti2 STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=COLVAR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab48,be0.bias STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BIAS
