Project ID: plumID:26.005
Source: plumed_S4_CD2AP_SH3-2.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_S4_CD2AP_SH3-2.dat — CRYPTAD # WTMetaD for CD2AP SH3-2 domain (S4) # 2 CVs: RT-loop flank (Site1) and groove (Site2) jaw distances # # Confirmed GROMACS atom indices (1-based, Cα): # cv_site1: GLU-124 = 238 | LEU-129 = 314 (ref dist = 1.347 nm) # cv_site2: LYS-114 = 61 | TYR-119 = 153 (ref dist = 1.267 nm) # # Note on residue numbering: residues 114–129 use the CD2AP full-protein # sequence numbers. The construct starts at ~residue 109; atom indices are # low (61, 153, 238, 314) because the construct is short (~62 residues). # # BEFORE RUNNING: # 1. Verify WHOLEMOLECULES atom range (estimate: SH3-2 construct ~62 residues # × ~15 atoms/res ≈ 930 atoms; adjust ENTITY0 upper bound accordingly). # 2. Compute nc_threshold from last 50 ns of production MD.
# ── PBC molecule reconstruction ─────────────────────────────────────────────── # CD2AP SH3-2 domain construct: ~62 residues × ~15 atoms/res ≈ 930 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=1-1000 # ── Biased collective variables ───────────────────────────────────────────────
# Site1 RT-loop flank jaw (GLU-124 Cα ↔ LEU-129 Cα) cv_site1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=238,314 # Site2 groove jaw (LYS-114 Cα ↔ TYR-119 Cα) cv_site2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=61,153 # ── 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 (37.0,27.26,30.56) # (residues ~120–132) and Site2 centroid (28.4,20.88,26.86) # (residues ~110–122, groove residues — functional interface, EXCLUDE). # Step 3: Stable core estimate for CD2AP SH3-2: β-barrel core residues # away from RT-loop (~residues 109–113 and 130–170 in full-protein numbering). # → translate to Cα atom indices with gmx_mpi select. # Step 4: AT = 0.80 × nc_mean. 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 — SH3 jaw distances ~1.3 nm; tune after 1 ns test. # 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_site2 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_site1,cv_site2,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