Project ID: plumID:26.005
Source: plumed_S2_BIN1_SH3.dat
Originally used with PLUMED version: 2.9
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
# plumed_S2_BIN1_SH3.dat — CRYPTAD # WTMetaD for BIN1 SH3 domain (S2) # 2 CVs: lateral-face pocket jaw distances for Site4 and Site5 # # Confirmed GROMACS atom indices (1-based, Cα): # cv_site4: PRO-6 = 92 | LYS-67 = 1050 (ref dist = 1.260 nm) # cv_site5: GLU-56 = 862 | LYS-64 = 994 (ref dist = 1.290 nm) # # BEFORE RUNNING: # 1. Verify WHOLEMOLECULES atom range (estimate: ~1050 atoms for SH3 domain # protein; adjust ENTITY0 upper bound from: gmx_mpi dump -s meta.tpr | grep natoms) # 2. Compute nc_threshold from last 50 ns of production MD (see TODO below).
# ── PBC molecule reconstruction ─────────────────────────────────────────────── # BIN1 SH3 domain ~70 residues × 15 atoms/res ≈ 1050 protein atoms. # Solvation follows; 1-1200 safely covers the full protein. 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=1-1200 # ── Biased collective variables ───────────────────────────────────────────────
# Site4 lateral-face jaw (PRO-6 Cα ↔ LYS-67 Cα) cv_site4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=92,1050 # Site5 lateral-face jaw (GLU-56 Cα ↔ LYS-64 Cα) cv_site5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=862,994 # ── Native contact restraint (unfolding guard) ──────────────────────────────── # TODO — required before production run (leave commented for 1 ns test): # Step 1: Compute stable Cα–Cα contact pairs (<0.8 nm, >80% occupancy) # from last 50 ns of production MD (see S1 file for method). # Step 2: Exclude residues within 12 Å of Site4 centroid (21.76,32.28,32.98) # and Site5 centroid (24.98,25.30,35.80) — roughly residues 1–15 and 50–70. # Step 3: Stable core estimate for BIN1 SH3: residues 16–49 (β-barrel core) # → translate to Cα atom indices with gmx_mpi select. # Step 4: AT = 0.80 × nc_mean (last 50 ns). Uncomment below. # # nc: COORDINATION ... # GROUPA=CA_STABLE GROUPB=CA_STABLE # SWITCH={RATIONAL R_0=0.8 D_MAX=0.8 NN=6 MM=10} # ... # nc_wall: LOWER_WALLS ARG=nc AT=NC_THRESHOLD KAPPA=1000.0 EXP=2 OFFSET=0
# ── Well-tempered metadynamics ──────────────────────────────────────────────── # SIGMA=0.1,0.1 nm — tuned for SH3 jaw distances ~1.3 nm; # adjust after 1 ns test (target: σ ≈ thermal fluctuation amplitude of each CV) # T_eff = 10 × 310.15 = 3,101.5 K # PACE=500 → 2 ps Gaussian interval (dt=0.004 HMR) metad: METADUsed to performed metadynamics on one or more collective variables. More details ... ARGthe labels of the scalars on which the bias will act=cv_site4,cv_site5 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=0.1,0.1 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 FILE a file in which the list of added hills is stored=HILLS WALKERS_Nnumber of walkers=1 ...
# ── Output ──────────────────────────────────────────────────────────────────── PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv_site4,cv_site5,metad.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