Project ID: plumID:26.005
Source: plumed_S3_PICALM_ANTH.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_S3_PICALM_ANTH.dat — CRYPTAD # WTMetaD for PICALM ANTH domain (S3) # 2 CVs: PI(4,5)P2-loop face pocket jaw distances for Site1 and Site4 # # Confirmed GROMACS atom indices (1-based, Cα): # cv_site1: LEU-131 = 1822 | ARG-139 = 1950 (ref dist = 1.234 nm) # cv_site4: ASP-203 = 2979 | SER-248 = 3753 (ref dist = 1.544 nm) # # BEFORE RUNNING: # 1. Verify WHOLEMOLECULES atom range (estimate: ANTH domain ~270 residues # × ~15 atoms/res ≈ 4050 protein atoms; adjust ENTITY0 upper bound). # 2. Compute nc_threshold from last 50 ns of production MD (see TODO below).
# ── PBC molecule reconstruction ─────────────────────────────────────────────── # PICALM ANTH domain ~270 residues × 15 atoms/res ≈ 4050 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=1-4500 # ── Biased collective variables ───────────────────────────────────────────────
# Site1 PIP2-loop face jaw (LEU-131 Cα ↔ ARG-139 Cα) cv_site1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1822,1950 # Site4 PIP2-loop face jaw (ASP-203 Cα ↔ SER-248 Cα) cv_site4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2979,3753 # ── 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. # Step 2: Exclude residues within 12 Å of Site1 centroid (41.26,42.15,42.59) # (residues ~125–145) and Site4 centroid (49.25,55.70,53.12) # (residues ~195–255, PIP2-binding loop region — functional interface, # EXCLUDE per §9 rule c: these are expected to move under bias). # Step 3: Stable core estimate for PICALM ANTH: residues away from PIP2 loop, # roughly residues 1–120 and 160–195. # → 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 — tuned for ANTH jaw distances ~1.2–1.5 nm; # cv_site4 ref dist = 1.544 nm; consider SIGMA=0.1,0.15 after 1 ns test. # T_eff = 10 × 310.15 = 3,101.5 K # PACE=500 → 2 ps Gaussian interval (dt=0.004 HMR) # # Multiple-walker WTMetaD recommended for PICALM (larger domain, §9 Step 3.3): # Add WALKERS_N=2 WALKERS_ID=0/1 WALKERS_DIR=./ WALKERS_RSTRIDE=100 # to both walkers' METAD blocks. 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=0.1,0.1 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_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