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 DISTANCE COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-338 LABELa label for the action so that its output can be referenced in the input to other actions=p1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=339-676 LABELa label for the action so that its output can be referenced in the input to other actions=p2 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p1,p2 LABELa label for the action so that its output can be referenced in the input to other actions=d
# FOUR COARSE GRAINED BEADS, EVERY 5 ISH RESIDUES COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-92 LABELa label for the action so that its output can be referenced in the input to other actions=B1_1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=93-170 LABELa label for the action so that its output can be referenced in the input to other actions=B2_1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=171-255 LABELa label for the action so that its output can be referenced in the input to other actions=B3_1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=256-338 LABELa label for the action so that its output can be referenced in the input to other actions=B4_1
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=339-430 LABELa label for the action so that its output can be referenced in the input to other actions=B1_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=431-508 LABELa label for the action so that its output can be referenced in the input to other actions=B2_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=509-593 LABELa label for the action so that its output can be referenced in the input to other actions=B3_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=594-676 LABELa label for the action so that its output can be referenced in the input to other actions=B4_2
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B1_1,B1_2 LABELa label for the action so that its output can be referenced in the input to other actions=B11 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B1_1,B2_2 LABELa label for the action so that its output can be referenced in the input to other actions=B12 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B1_1,B3_2 LABELa label for the action so that its output can be referenced in the input to other actions=B13 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B1_1,B4_2 LABELa label for the action so that its output can be referenced in the input to other actions=B14
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B2_1,B1_2 LABELa label for the action so that its output can be referenced in the input to other actions=B21 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B2_1,B2_2 LABELa label for the action so that its output can be referenced in the input to other actions=B22 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B2_1,B3_2 LABELa label for the action so that its output can be referenced in the input to other actions=B23 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B2_1,B4_2 LABELa label for the action so that its output can be referenced in the input to other actions=B24
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B3_1,B1_2 LABELa label for the action so that its output can be referenced in the input to other actions=B31 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B3_1,B2_2 LABELa label for the action so that its output can be referenced in the input to other actions=B32 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B3_1,B3_2 LABELa label for the action so that its output can be referenced in the input to other actions=B33 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B3_1,B4_2 LABELa label for the action so that its output can be referenced in the input to other actions=B34
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B4_1,B1_2 LABELa label for the action so that its output can be referenced in the input to other actions=B41 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B4_1,B2_2 LABELa label for the action so that its output can be referenced in the input to other actions=B42 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B4_1,B3_2 LABELa label for the action so that its output can be referenced in the input to other actions=B43 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=B4_1,B4_2 LABELa label for the action so that its output can be referenced in the input to other actions=B44
# Phosphate Ions COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=677-682 LABELa label for the action so that its output can be referenced in the input to other actions=OP1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=683-688 LABELa label for the action so that its output can be referenced in the input to other actions=OP2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=689-694 LABELa label for the action so that its output can be referenced in the input to other actions=OP3 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=695-700 LABELa label for the action so that its output can be referenced in the input to other actions=OP4 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=701-706 LABELa label for the action so that its output can be referenced in the input to other actions=OP5 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=707-712 LABELa label for the action so that its output can be referenced in the input to other actions=OP6
# Head Groups of Positively Charged Sidechains 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 LABELa label for the action so that its output can be referenced in the input to other actions=K3_1 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 LABELa label for the action so that its output can be referenced in the input to other actions=K4_1 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 LABELa label for the action so that its output can be referenced in the input to other actions=K12_1 #NZ,HZ123 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 LABELa label for the action so that its output can be referenced in the input to other actions=K15_1 #NZ,HZ123 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=264-271 LABELa label for the action so that its output can be referenced in the input to other actions=R16_1 #HE, CZ, N+H COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=285-292 LABELa label for the action so that its output can be referenced in the input to other actions=R17_1 #HE, CZ, N+H
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=386-389 LABELa label for the action so that its output can be referenced in the input to other actions=K3_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=408-411 LABELa label for the action so that its output can be referenced in the input to other actions=K4_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=536-539 LABELa label for the action so that its output can be referenced in the input to other actions=K12_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=585-588 LABELa label for the action so that its output can be referenced in the input to other actions=K15_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=602-609 LABELa label for the action so that its output can be referenced in the input to other actions=R16_2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=623-630 LABELa label for the action so that its output can be referenced in the input to other actions=R17_2
# Coordination with Phosphate COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=K3_1,K4_1,K12_1,K15_1,R16_1,R17_1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OP1,OP2,OP3,OP4,OP5,OP6 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=1 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 LABELa label for the action so that its output can be referenced in the input to other actions=IONCL1 COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=K3_2,K4_2,K12_2,K15_2,R16_2,R17_2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OP1,OP2,OP3,OP4,OP5,OP6 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=1 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 LABELa label for the action so that its output can be referenced in the input to other actions=IONCL2
# Radius of Gyration: backbone N atoms for each chain 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=7,21,35,57,79,93,106,120,144,158,171,185,207,220,234,256,277,298,317 LABELa label for the action so that its output can be referenced in the input to other actions=rg1 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=345,359,373,395,417,431,444,458,482,496,509,523,545,558,572,594,615,636,655 LABELa label for the action so that its output can be referenced in the input to other actions=rg2
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=6.5 KAPPAthe force constant for the wall=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
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=B11,B12,B13,B14,B21,B22,B23,B24,B31,B32,B33,B34,B41,B42,B43,B44,IONCL1,IONCL2,rg1,rg2 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=0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.02,0.05,0.05 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.6,0.6 HEIGHTthe height of the Gaussian hills, one for all biases=2.0 PACEthe frequency for hill addition, one for all biases=1000 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=54 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=-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 GRID_MAXthe upper bounds for the grid=15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,36,36,15,15 FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../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 ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVAR