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These benchmarks may be of use in comparing machines and programs.
Two cases are considered: a "small," 274-atom solute in a large
periodic bath of water molecules and ions; and a "large," 4282-atom
molecule in vacuum. For simplicity, both systems are DNA. Each model
is generated in periodic B form according to Langridge, and is not
proprietary in any way.

For people who have Amber, the file BenchDNA_Amber.tar.Z can be
used. Obtain it by binary ftp, uncompress it, and extract the
files using tar:

	ftp> bin
	ftp> get BenchDNA_Amber.tar.Z
	ftp> quit
	% uncompress BenchDNA_Amber.tar
	% tar xvof BenchDNA_Amber.tar

Users of other programs who want to import the models should obtain
the PDB format files:

	ftp> bin
	ftp> get BenchDNA1.pdb.Z
	ftp> get BenchDNA2.pdb.Z
	ftp> quit
	% uncompress BenchDNA1.pdb BenchDNA2.pdb

Here is a description of the conditions for running the two cases:

		1st					2nd

	   DNA hexamer in periodic 	        68 DNA base pairs in vacuum.
	   water box, constant volume.	        4282 atoms, 10A cutoff on all
	   7682 atoms: 274 dna, 10 	        nonbonded pairs. Distance-
	   counterions, 2466 waters.		dependent dielectric.
	   All solute interactions;
	   8A cutoff otherwise. Constant

In both cases, 100 steps of minimization and 100 steps of dynamics are
run. In the Amber version, two programs are used for this, and a third
program is used for 100 steps of free energy perturbation (CYT->quasi_URA).

The latest version of the results for Amber can be obtained by request

Bill Ross, UCSF 1992

Modified: Thu Aug 20 16:00:00 1992 GMT
Page accessed 12434 times since Sat Apr 17 21:25:59 1999 GMT