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 dielectric. 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 to amber-request@cgl.ucsf.edu. Bill Ross, UCSF 1992 ross@cgl.ucsf.edu