*** 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

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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.


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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.


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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.



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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.