Project ID: plumID:26.005
Source: plumed_S5_CD2AP_SH3-1.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_S5_CD2AP_SH3-1.dat — CRYPTAD # WTMetaD for CD2AP SH3-1 domain (S5) # 2 CVs: groove face (Site1) and RT-loop flank (Site4) jaw distances # # Confirmed GROMACS atom indices (1-based, Cα): # cv_site1: ASN-29 = 460 | GLY-45 = 720 (ref dist = 1.224 nm) # cv_site4: GLY-24 = 376 | PHE-50 = 799 (ref dist = 1.496 nm) # # Note: CD2AP SH3-1 construct is numbered from residue 1 (unlike SH3-2). # Atom indices are consistent with ~50 residues × ~16 atoms/res before PHE-50. # # BEFORE RUNNING: # 1. Verify WHOLEMOLECULES atom range (estimate: SH3-1 construct ~70 residues # × ~15 atoms/res ≈ 1050 atoms; adjust ENTITY0 upper bound accordingly). # 2. Compute nc_threshold from last 50 ns of production MD.
# ── PBC molecule reconstruction ─────────────────────────────────────────────── # CD2AP SH3-1 domain construct: ~70 residues × ~15 atoms/res ≈ 1050 protein atoms. 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 ───────────────────────────────────────────────
# Site1 groove-face jaw (ASN-29 Cα ↔ GLY-45 Cα) cv_site1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=460,720 # Site4 RT-loop flank jaw (GLY-24 Cα ↔ PHE-50 Cα) cv_site4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=376,799 # ── Native contact restraint (unfolding guard) ──────────────────────────────── # TODO — required before production run (leave commented for 1 ns test): # Step 1: Compute stable Cα–Cα contacts (<0.8 nm, >80% occupancy) # from last 50 ns of production MD. # Step 2: Exclude residues within 12 Å of Site1 centroid (29.04,28.65,19.88) # (residues ~24–50, groove face — functional interface, EXCLUDE per §9 rule c) # and Site4 centroid (32.74,36.65,29.05) (residues ~19–55, RT-loop). # Step 3: With both pockets near the binding groove, the stable core is the # β-barrel far from the groove (~residues 1–20 and 55–70). # → translate to Cα atom indices with gmx_mpi select. # Step 4: AT = 0.80 × nc_mean. Uncomment below. # NOTE: For S5, the stable core is small; KAPPA may need to be # reduced (500–800) if the LOWER_WALLS fires spuriously. # # 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=0.1,0.15 nm — cv_site4 ref dist = 1.496 nm (wider range); tune after 1 ns. # 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_site1,cv_site4 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 SIGMAthe widths of the Gaussian hills=0.1,0.15 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_site1,cv_site4,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