Project ID: plumID:23.023
Source: silicate_files/plumed.dat
Originally used with PLUMED version: 2.8
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
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## RESTART
# Silicate Ions SIL1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=339-346 SIL2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=347-354 SIL3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=355-362 SIL4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=363-370 SIL5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=371-378 SIL6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=379-386 # Lysine head groups K1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=48-51 K2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=70-73 K3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=198-201 K4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=247-250 # Arginine head groups R1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=266-271 R2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=287-292 # Coordination with silicate ions COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=K1,K2,K3,K4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SIL1,SIL2,SIL3,SIL4,SIL5,SIL6 R_0The r_0 parameter of the switching function=0.5 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=100 NN The n parameter of the switching function =20 MM The m parameter of the switching function; 0 implies 2*NN=40 LABELa label for the action so that its output can be referenced in the input to other actions=KCN COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=R1,R2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SIL1,SIL2,SIL3,SIL4,SIL5,SIL6 R_0The r_0 parameter of the switching function=0.5 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=100 NN The n parameter of the switching function =20 MM The m parameter of the switching function; 0 implies 2*NN=40 LABELa label for the action so that its output can be referenced in the input to other actions=RCN
# Radius of Gyration: All CA atoms GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=16,30,52,74,88,101,115,139,153,166,180,202,215,229,251,272,293,312,331 LABELa label for the action so that its output can be referenced in the input to other actions=rg
PBMETADUsed to performed Parallel Bias metadynamics. More details ... WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR ARGthe labels of the scalars on which the bias will act=KCN,RCN,rg SIGMAthe widths of the Gaussian hills=200.0 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.02,0.02,0.05 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.5,0.5,0.6 HEIGHTthe height of the Gaussian hills, one for all biases=2.0 #kJ/mol PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=16 # Sqrt[cv]*8 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 LABELa label for the action so that its output can be referenced in the input to other actions=PBMETAD GRID_MINthe lower bounds for the grid=-0.5,-0.5,-0.5 GRID_MAXthe upper bounds for the grid=25.0,13.0,15.0 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS.KCN,../HILLS.RCN,../HILLS.rg ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=KCN,RCN,rg,PBMETAD.bias STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR