Hi everyone. I’m working in bioinform. lab. and we have cluster for molecular dynamics, with protein like subject. So we use gromacs\amber soft, but they works with cpu only. I see now, that Folding@home explode GPU in full volume, and name it - GroGPU (gromacs).
They use CUDA? How to modify our soft (gromacs\amber) for GPU? >.<
Whatever you try, they’ve had a head start for more than 2 years. ;)
You’re in luck! There’s already Gromacs and Amber libraries for both CPU and CUDA. And many more…
[url=“SimTK: OpenMM: Project Home”]https://simtk.org/home/openmm[/url]
You’re in luck! There’s already Gromacs and Amber libraries for both CPU and CUDA. And many more…
[url=“SimTK: OpenMM: Project Home”]https://simtk.org/home/openmm[/url]
That’s actually wonderful. Didn’t know they had intended to release their code.
No problem. I wouldn’t have known about it except for Nvision, where Vijay Pande talked about it briefly. He was really eager to talk to people about the library and tweak its API for easier use… I’m sure if you email him he’ll be receptive.
Oops, looks like you’re right, they’re just CPU versions for now… CUDA still in beta. But obviously coming.
shameless plug HOOMD [url=“http://www.ameslab.gov/hoomd”]http://www.ameslab.gov/hoomd[/url] already does general purpose MD entirely on the GPU. It is modeled more after LAMMPS, so a gromacs user will not find the interface familiar. The current version of HOOMD is appropriate for coarse-grained models: over the next few releases we will be adding features needed for all-atom simulations.
MisterAnderson42 - thanks
Someone knows, about Replica Exchange Method and can it use GPU clusters?
google say its based on GroST (80 core) [url=“http://folding.stanford.edu/English/FAQ-gromacs#ntoc14”]http://folding.stanford.edu/English/FAQ-gromacs#ntoc14[/url]
Replica exchange is pretty simple. It could be implemented easily on a GPU cluster where each node (or each GPU) runs a single replica.
There is also “Ascalaph Liquid GPU” that made MD in AMBER94.
[url=“http://www.agilemolecule.com/Ascalaph/Packages.html”]http://www.agilemolecule.com/Ascalaph/Packages.html[/url]
Unfortunately it does not support Replica Exchange yet.