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> get BenchDNA_Amber.tar.Z
% 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> get BenchDNA1.pdb.Z
ftp> get BenchDNA2.pdb.Z
% uncompress BenchDNA1.pdb BenchDNA2.pdb
Here is a description of the conditions for running the two cases:
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 firstname.lastname@example.org