I am looking for an open source GPGPU project for protein folding (CUDA/OpenCL). Would you please giving me some suggestions?
Thanks
I am looking for an open source GPGPU project for protein folding (CUDA/OpenCL). Would
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I am looking for an open source GPGPU project for protein folding (CUDA/OpenCL). Would you please giving me some suggestions?
Thanks
Folding@home is probably the largest GPU-based protein folding project by far. So you would probably do well to use whatever they use: Folding@home open source FAQ. That appears to be a custom version of Gromacs and OpenMM.
A full list of software like this is here: Molecular modeling on GPUs. Notable software packages in addition to GROMACS/OpenMM include NAMD (which has been around since 1995), and ACEMD.
These can be classified into molecular dynamics (using empirical potential fields), ab-initio (using quantum mechanics), and hybrid. None of these are protein-folding-specific, but most of the molecular dynamics packages can handle protein-folding-sized problems. The ab-initio packages aren’t there yet, but getting close.