Project ID: plumID:23.023
Source: dimer_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 ## ENERGY LABEL=energy
# DIMER-DIMER DISTANCECOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-338the list of atoms which are involved the virtual atom's definitionLABEL=p1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=339-676the list of atoms which are involved the virtual atom's definitionLABEL=p2a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=p1,p2the pair of atom that we are calculating the distance betweenLABEL=da label for the action so that its output can be referenced in the input to other actions
# FOUR COARSE GRAINED BEADS, EVERY 5 ISH RESIDUESCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-92the list of atoms which are involved the virtual atom's definitionLABEL=B1_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=93-170the list of atoms which are involved the virtual atom's definitionLABEL=B2_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=171-255the list of atoms which are involved the virtual atom's definitionLABEL=B3_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=256-338the list of atoms which are involved the virtual atom's definitionLABEL=B4_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=339-430the list of atoms which are involved the virtual atom's definitionLABEL=B1_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=431-508the list of atoms which are involved the virtual atom's definitionLABEL=B2_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=509-593the list of atoms which are involved the virtual atom's definitionLABEL=B3_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=594-676the list of atoms which are involved the virtual atom's definitionLABEL=B4_2a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B1_1,B1_2the pair of atom that we are calculating the distance betweenLABEL=B11a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B1_1,B2_2the pair of atom that we are calculating the distance betweenLABEL=B12a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B1_1,B3_2the pair of atom that we are calculating the distance betweenLABEL=B13a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B1_1,B4_2the pair of atom that we are calculating the distance betweenLABEL=B14a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B2_1,B1_2the pair of atom that we are calculating the distance betweenLABEL=B21a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B2_1,B2_2the pair of atom that we are calculating the distance betweenLABEL=B22a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B2_1,B3_2the pair of atom that we are calculating the distance betweenLABEL=B23a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B2_1,B4_2the pair of atom that we are calculating the distance betweenLABEL=B24a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B3_1,B1_2the pair of atom that we are calculating the distance betweenLABEL=B31a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B3_1,B2_2the pair of atom that we are calculating the distance betweenLABEL=B32a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B3_1,B3_2the pair of atom that we are calculating the distance betweenLABEL=B33a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B3_1,B4_2the pair of atom that we are calculating the distance betweenLABEL=B34a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B4_1,B1_2the pair of atom that we are calculating the distance betweenLABEL=B41a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B4_1,B2_2the pair of atom that we are calculating the distance betweenLABEL=B42a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B4_1,B3_2the pair of atom that we are calculating the distance betweenLABEL=B43a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=B4_1,B4_2the pair of atom that we are calculating the distance betweenLABEL=B44a label for the action so that its output can be referenced in the input to other actions
# Phosphate IonsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=677-682the list of atoms which are involved the virtual atom's definitionLABEL=OP1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=683-688the list of atoms which are involved the virtual atom's definitionLABEL=OP2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=689-694the list of atoms which are involved the virtual atom's definitionLABEL=OP3a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=695-700the list of atoms which are involved the virtual atom's definitionLABEL=OP4a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=701-706the list of atoms which are involved the virtual atom's definitionLABEL=OP5a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=707-712the list of atoms which are involved the virtual atom's definitionLABEL=OP6a label for the action so that its output can be referenced in the input to other actions
# Head Groups of Positively Charged SidechainsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=48-51the list of atoms which are involved the virtual atom's definitionLABEL=K3_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=70-73the list of atoms which are involved the virtual atom's definitionLABEL=K4_1a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=198-201the list of atoms which are involved the virtual atom's definitionLABEL=K12_1 #NZ,HZ123a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=247-250the list of atoms which are involved the virtual atom's definitionLABEL=K15_1 #NZ,HZ123a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=264-271the list of atoms which are involved the virtual atom's definitionLABEL=R16_1 #HE, CZ, N+Ha label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=285-292the list of atoms which are involved the virtual atom's definitionLABEL=R17_1 #HE, CZ, N+Ha label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=386-389the list of atoms which are involved the virtual atom's definitionLABEL=K3_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=408-411the list of atoms which are involved the virtual atom's definitionLABEL=K4_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=536-539the list of atoms which are involved the virtual atom's definitionLABEL=K12_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=585-588the list of atoms which are involved the virtual atom's definitionLABEL=K15_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=602-609the list of atoms which are involved the virtual atom's definitionLABEL=R16_2a label for the action so that its output can be referenced in the input to other actionsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=623-630the list of atoms which are involved the virtual atom's definitionLABEL=R17_2a label for the action so that its output can be referenced in the input to other actions
# Coordination with PhosphateCOORDINATIONCalculate coordination numbers. More detailsGROUPA=K3_1,K4_1,K12_1,K15_1,R16_1,R17_1First list of atomsGROUPB=OP1,OP2,OP3,OP4,OP5,OP6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listLABEL=IONCL1a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=K3_2,K4_2,K12_2,K15_2,R16_2,R17_2First list of atomsGROUPB=OP1,OP2,OP3,OP4,OP5,OP6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listLABEL=IONCL2a label for the action so that its output can be referenced in the input to other actions
# Radius of Gyration: backbone N atoms for each chainGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=7,21,35,57,79,93,106,120,144,158,171,185,207,220,234,256,277,298,317the group of atoms that you are calculating the Gyration Tensor forLABEL=rg1a label for the action so that its output can be referenced in the input to other actionsGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=345,359,373,395,417,431,444,458,482,496,509,523,545,558,572,594,615,636,655the group of atoms that you are calculating the Gyration Tensor forLABEL=rg2a label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dthe arguments on which the bias is actingAT=6.5the positions of the wallKAPPA=1000000the force constant for the wallLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRARG=B11,B12,B13,B14,B21,B22,B23,B24,B31,B32,B33,B34,B41,B42,B43,B44,IONCL1,IONCL2,rg1,rg2the input for this action is the scalar output from one or more other actionsSIGMA=200.0the widths of the Gaussian hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.05,0.05the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.6,0.6the upper bounds for the sigmas (in CV units) when using adaptive hillsHEIGHT=2.0the height of the Gaussian hills, one for all biasesPACE=1000the frequency for hill addition, one for all biasesBIASFACTOR=54use well tempered metadynamics with this bias factor, one for all biasesTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=PBMETADa label for the action so that its output can be referenced in the input to other actionsGRID_MIN=-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1the lower bounds for the gridGRID_MAX=15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,36,36,15,15the upper bounds for the gridFILE=../HILLS_B11,../HILLS_B12,../HILLS_B13,../HILLS_B14,../HILLS_B21,../HILLS_B22,../HILLS_B23,../HILLS_B24,../HILLS_B31,../HILLS_B32,../HILLS_B33,../HILLS_B34,../HILLS_B41,../HILLS_B42,../HILLS_B43,../HILLS_B44,../HILLS_IONCL1,../HILLS_IONCL2,../HILLS_RG1,../HILLS_RG2 ... PBMETADfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=250the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities