Project ID: plumID:24.003
Source: plumed_nest/diff_sequences/CH22/plumed.dat
Originally used with PLUMED version: 2.8-mod
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
tested onv2.10
tested onmaster
#! vim:ft=plumed
## RESTART

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=1-636 # CHAIN ONE AND RESIDUE BEFORE LINKER COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-304 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=1-30 LABELa label for the action so that its output can be referenced in the input to other actions=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=280-304 LABELa label for the action so that its output can be referenced in the input to other actions=r14
# CHAIN TWO AND RESIDUE AFTER LINKER COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=339-636 LABELa label for the action so that its output can be referenced in the input to other actions=p2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=339-364 LABELa label for the action so that its output can be referenced in the input to other actions=r16 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=614-636 LABELa label for the action so that its output can be referenced in the input to other actions=r30
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 DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=r14,r16 LABELa label for the action so that its output can be referenced in the input to other actions=in DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=r1,r30 LABELa label for the action so that its output can be referenced in the input to other actions=FRET
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=1,31,64,89,122,148,177,202,225,251,280,339,365,398,423,456,482,511,536,559,585,614 LABELa label for the action so that its output can be referenced in the input to other actions=rg 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=1,31,64,89,122,148,177,202,225,251,280 LABELa label for the action so that its output can be referenced in the input to other actions=rg_1
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=339,365,398,423,456,482,511,536,559,585,614 LABELa label for the action so that its output can be referenced in the input to other actions=rg_2
# hydrophobic 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=31-63 LABELa label for the action so that its output can be referenced in the input to other actions=H1 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=89-121 LABELa label for the action so that its output can be referenced in the input to other actions=H2 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=148-176 LABELa label for the action so that its output can be referenced in the input to other actions=H3 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=202-224 LABELa label for the action so that its output can be referenced in the input to other actions=H4 COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=251-279 LABELa label for the action so that its output can be referenced in the input to other actions=H5
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=365-397 LABELa label for the action so that its output can be referenced in the input to other actions=H1_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=423-455 LABELa label for the action so that its output can be referenced in the input to other actions=H2_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=482-510 LABELa label for the action so that its output can be referenced in the input to other actions=H3_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=536-558 LABELa label for the action so that its output can be referenced in the input to other actions=H4_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=585-613 LABELa label for the action so that its output can be referenced in the input to other actions=H5_2
COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=H1,H2,H3,H4,H5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H1_2,H2_2,H3_2,H4_2,H5_2 R_0The r_0 parameter of the switching function=1.9 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.2 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=80 LABELa label for the action so that its output can be referenced in the input to other actions=COORD COORDINATIONCalculate coordination numbers. More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=H1,H2,H3,H4,H5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H5_2,H4_2,H3_2,H2_2,H1_2 R_0The r_0 parameter of the switching function=1.9 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.2 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=80 LABELa label for the action so that its output can be referenced in the input to other actions=PAIR
#INCLUDE FILE=prmsd.dat INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=dihedral.dat
# to ensure passing on PLUMED nest, we've commented out some lines in this file # needed to run the steered MD. these lines utilize a bespoke CV known as # ToidRMSD--check out our previous work to read more about the CV or contact # Dr. Jim Pfaendtner at pfaendtner@ncsu.edu for more information
#MOVINGRESTRAINT ... # ARG=d,a0,b0 # STEP0=50000 AT0=2,0.09,0.03 KAPPA0=1000,100,100 # STEP1=2550000 AT1=4,9,9 KAPPA1=2500,2500,2500 # STEP2=8825000 KAPPA2=0,2500,2500 # STEP3=25100000 KAPPA3=0,2500,2500 # STEP4=37500000 KAPPA4=0,0,0 #... MOVINGRESTRAINT
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=1000 FILEthe name of the file on which to output these quantities=COLVAR