                    Desmond/GPU Benchmark Systems                       D. E. 
Shaw Research                         April 29, 2021
 This directory contains a README.txt file, a copy of the license file, and the 
structure files used as benchmarks in the Desmond/GPU Technical Report [1].  
The benchmarks are further described in the table below.
 The structure files are provided in Desmond (dms) format with standard 
hydrogen masses.  Conversions for Hydrogen Mass Repartitioning, for tiling 
stmv, or to the mae format can be implemented using tools from the msys package 
available via github [2].
 [1] M. Bergdorf, et al., "Desmond/GPU Performance as of April 2021," 
DESRES/TR--2021-01, https://deshawresearch.com/publications.html
 [2] D. E. Shaw Research github repository, https://github.com/DEShawResearch
 |       File name       |  Chemical system  |  # atoms  | Forcefield      |    
Source     | 
|-----------------------|-------------------|-----------|-----------------|-----
----------| | dhfr_20210429.dms     | DHFR              |    23,558 | 
Amber99SB*-ILDN | PDB 5DFR (*)  | | apoa1_20210429.dms    | ApoA1             | 
   92,196 | CHARMM36        | UIUC (**)     | | f1atpase_20210429.dms | ATpase  
          | 327,506 | CHARMM          | UIUC (**)     | | stmv_20210429.dms     
| STMV | 1,066,628 | CHARMM          | UIUC (***)    | | ribosome_20210429.dms 
| Ribosome          | 2,180,503 | Amber99SB-ILDN  | PDB 4V7A      |
 (*) Amber GPU benchmarks, http://ambermd.org/gpus16/benchmarks.htm
 (**) NAMD utilities, http://www.ks.uiuc.edu/Research/namd/utilities/ Emad 
Tajkhorshid, Aleksei Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James 
C. Phillips, Fangqiang Zhu, and Klaus Schulten. "Large scale simulation of 
protein mechanics and function", 2003, Advances in Protein Chemistry, vol. 66, 
195-247.
 (***) NAMD utilities, http://www.ks.uiuc.edu/Research/namd/utilities/ P. L. 
Freddolino, A. S. Arkhipov, S. B. Larson, A. McPherson, and K. Schulten, 
"Molecular dynamics simulations of the complete satellite tobacco mosaic 
virus", 2006, Structure 14, 437-449.
