Project ID: plumID:24.003
Source: plumed_nest/diff_sequences/CH30/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=1-826 # 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=1-399 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=376-399 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=434-826 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=434-458 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=804-826 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=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376,434,459,492,516,540,573,598,624,653,677,701,724,749,775,804 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=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376 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=434,459,492,516,540,573,598,624,653,677,701,724,749,775,804 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=112-144 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=196-224 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=273-295 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=347-375 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=459-491 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=540-572 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=624-652 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=701-723 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=775-803 LABELa label for the action so that its output can be referenced in the input to other actions=H5_2
COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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. This action has hidden defaults. 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=4,13,13 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