*** Welcome to our GAAC DNA data repository! See also the newer force *** field comparison data also on http://amber.utah.edu Here are results from the simulation of the "GAAC" 18-mer sequence on various resources including DE Shaw's Anton machine at PSC, Keeneland/KIDS from NICS/GaTech/XSEDE, and NSF Blue Waters. d(GCACGAACGAACGAACGC) Publications describing this work are: R Galindo-Murillo, DR Roe, and TE Cheatham, III. "On the absence of intrahelical DNA dynamics on the micros to ms timescale." Nature Commun. 5:5152 (2014) doi: 10.1038/ncomms6152. R Galindo-Murillo, DR Roe, and TE Cheatham, III. "Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)." Biochimica Biophys. Acta 1850, 1041-1058 (2015) doi: 10.1016/j.bbagen.2014.09.007. At the top level are trajectories processed via CPPTRAJ to remove solvent or solvent and ions. CPPTRAJ is part of AmberTools and is available at http://www.ambermd.org. Most simulations were performed with the AMBER ff12 force field (ff99 + parmbsc0) in SPC/E water with Smith/Dang ~100 mM KCl similar to the ABC simulations. Additional simulations (C36) were with the CHARMM C36 force field in CHARMM TIP3P water with equivalent salt concentration (using CHARMM KCl parameters). For more details, e-mail: tec3@utah.edu Anton - ~44 microsecond MD simulation on Anton Anton-initial - ~11 microsecond MD simulation on Anton ensemble - ~20+ microsecond aggregated AMBER GPU simulations ensemble-c36 - ~20+ microsecond aggregated AMBER GPU simulations w/ C36 __________________________________________________________________ Anton, ~44 microsecond run, at 50 ps intervals GAAC-ions.topo - AMBER parameter/topology with DNA + ions only Anton-GAAC-ions.crd - AMBER ascii trajectory, DNA + ions only GAAC-invacuo.topo - AMBER parameter/topology with DNA only Anton-GAAC-invacuo.crd - AMBER ascii trajectory, DNA only Anton-initial-avg_0-10us.pdb - Reference PDB 10 microsecond straight coordinate average from fit to first frame from initial 11 microsecond Anton MD simulation. More details: AMBER prmtop converted into format appropriate for Anton. Anton data converted to DCD format by VMD and then processed by cpptraj. __________________________________________________________________ Anton-initial, ~11 microsecond run, at 50 ps intervals Anton-initial-data/ - The original/raw data (see _README_) GAAC-ions.topo - AMBER parameter/topology with DNA + ions only Anton-initial-ions.crd - AMBER ascii trajectory, DNA + ions only GAAC-invacuo.topo - AMBER parameter/topology with DNA only Anton-initial-invacuo.crd - AMBER ascii trajectory, DNA only Anton-initial-avg_0-10us.pdb - Reference PDB 10 microsecond straight coordinate average from fit to first frame from initial 11 microsecond Anton MD simulation. More details: AMBER prmtop converted into format appropriate for Anton. Anton data converted to DCD format by VMD and then processed by cpptraj. __________________________________________________________________ ensemble, ~20+ microsecond aggregated runs, at 50 ps intervals GAAC-ions.topo - AMBER parameter/topology with DNA + ions only ensemble-ions.crd - AMBER ascii trajectory, DNA + ions only GAAC-invacuo.topo - AMBER parameter/topology with DNA only ensemble-invacuo.crd - AMBER ascii trajectory, DNA only More details: 100 independent AMBER GPU simulations were performed on KIDS/Keeneland of the DNA each with different initial randomized ions positions. The MD trajectories were aggregrated together after removing the first 100 ns of each simulation. __________________________________________________________________ ensemble-c36, ~30+ microsecond aggregated runs, at 50 ps intervals GAAC_all36_na_cio.topo - CHARMM C36 in AMBER parameter/topology format with DNA and ions only ensemble-c36-ions.crd - AMBER ascii trajectory, DNA + ions only GAAC_all36_na_vac.topo - CHARMM C36 in AMBER parameter/topology format with DNA only ensemble-c36-invacuo.crd - AMBER ascii trajectory, DNA only More details: 100 independent AMBER GPU simulations were performed on Blue Waters of the DNA each with different initial randomized ions positions using the CHARMM C36 force field in CHARMM TIP3P water and ions. The MD trajectories were aggregrated together after removing the first 100 ns of each simulation.