Project ID: plumID:26.005
Source: plumed_S1_BIN1_BAR.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_S1_BIN1_BAR.dat — CRYPTAD # WTMetaD for BIN1 BAR homodimer (S1) # 2 CVs: concave-face inter-monomer jaw distance (CV1) + BAR long-axis hinge angle (CV2) # # Confirmed GROMACS atom indices (1-based, Cα): # CV1 jaw: A-TYR217 = 2595 | B-GLU178 = 5230 (ref dist = 4.000 nm) # CV2 hinge: A-THR172 = 1974 (tip_A) # B-ILE146 = 4682 (center / bend vertex) # B-GLU250 = 6384 (tip_B) # # BEFORE RUNNING: # 1. Verify WHOLEMOLECULES atom range (current estimate: 1–8000 covers the # BAR dimer protein heavy atoms; solvation atoms come after in CHARMM-GUI # topologies). Confirm with: # gmx_mpi dump -s meta.tpr 2>&1 | grep 'natoms' # Then adjust ENTITY0=1-N to match the last protein atom. # 2. Compute nc_threshold from last 50 ns of production MD (see TODO below). # 3. Temperature (TEMP=310.15) must match ref_t in meta.mdp. # # Reference: research plan §9 Step 3.3 (v1.3 template)
# ── PBC molecule reconstruction ─────────────────────────────────────────────── # Covers both BAR chains (A+B, ~430 res × 2 × ~9 heavy atoms = ~7700 atoms) # Adjust upper bound to the actual last protein atom from the topology. 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=1-8000 # ── Biased collective variables ───────────────────────────────────────────────
# CV1: inter-monomer concave jaw (A-TYR217 Cα ↔ B-GLU178 Cα) # Selected by geometric concave-face projection opposite to convex centroid. cv1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2595,5230 # CV2: BAR long-axis hinge angle (A-THR172 → B-ILE146 → B-GLU250) # tip_A → center (bend vertex) → tip_B — spans the full ~128 Å long axis. # PLUMED ANGLE order: ATOMS=tip_A,center,tip_B (same order as IDX_A,IDX_C,IDX_B) cv2: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1974,4682,6384 # ── Native contact restraint (unfolding guard) ──────────────────────────────── # Keeps the BAR dimer from denaturing under metadynamics bias. # # TODO — required before production run (leave commented for 1 ns test): # Step 1: Identify stable residue pairs from last 50 ns of production MD: # python -c " # import mdtraj as md, numpy as np # t = md.load('prod.xtc', top='prod.gro', stride=10) # t = t[-250:] # last 50 ns at 200 ps/frame stride # # Compute Cα–Cα contact occupancy at 0.8 nm; use mdtraj or MDAnalysis # " # Step 2: Exclude residues within 12 Å of pocket centroid (81.84,71.23,74.61) # → roughly residues A:200-220 and B:160-185 in the BAR concave face. # Step 3: Exclude tip residues (chain A: <175; chain B: >245 and <152) # Stable core range estimate: chain A residues 175–215, chain B residues 155–245 # → translate to Cα atom index ranges using gmx_mpi select: # gmx_mpi select -s meta.tpr -select 'name CA and chain A and resnr >= 175 and resnr <= 215' # Step 4: Set AT = 0.80 × nc_mean (20 % safety margin below equilibrium) # Step 5: Uncomment the nc: and nc_wall: lines below. # # Placeholder (disabled) — fill in GROUPA/GROUPB atom lists from Step 3 above: # nc: COORDINATION ... # GROUPA=CA_STABLE_ATOMS GROUPB=CA_STABLE_ATOMS # SWITCH={RATIONAL R_0=0.8 D_MAX=0.8 NN=6 MM=10} # ... # # LOWER_WALLS fires when nc drops below AT (prevents unfolding). # nc_wall: LOWER_WALLS ARG=nc AT=NC_THRESHOLD KAPPA=1000.0 EXP=2 OFFSET=0
# ── Well-tempered metadynamics ──────────────────────────────────────────────── # T_eff = BIASFACTOR × TEMP = 10 × 310.15 = 3,101.5 K # PACE=500 → deposit Gaussian every 500 × 0.004 ps = 2 ps (HMR dt=0.004) metad: METADUsed to performed metadynamics on one or more collective variables. More details ... ARGthe labels of the scalars on which the bias will act=cv1,cv2 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=0.3,0.05 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 ... # For multiple-walker WTMetaD (recommended for BIN1 — §9 Step 3.3): # Add to each walker's METAD block: # WALKERS_N=2 WALKERS_ID=0 (walker 1) or WALKERS_ID=1 (walker 2) # WALKERS_DIR=./ WALKERS_RSTRIDE=100 # Both walkers share the same HILLS file on Lustre/NFS.
# ── Output ──────────────────────────────────────────────────────────────────── # STRIDE=500 → write COLVAR every 500 × 0.004 ps = 2 ps # Once nc guard is active, add nc to ARG: ARG=cv1,cv2,nc,metad.bias PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv1,cv2,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 # ── Monitoring notes ────────────────────────────────────────────────────────── # 1. After 1 ns test: HILLS and COLVAR files must exist → PLUMED working. # 2. SIGMA tuning: inspect CV1 and CV2 fluctuations in the first ~5 ns # unbiased COLVAR columns; set SIGMA ~ 1× the thermal fluctuation width. # If CV1 fluctuates ±0.1 nm → SIGMA=0.1 is sufficient; 0.3 is conservative. # 3. Convergence: run plumed sum_hills --hills HILLS --stride 100 --mintozero # at t=67, 133, 200 ns; ΔΔF < 1 kJ/mol → converged FES (§9 Step 3.3).