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I want to build a new desktop PC for MD simulations of relatively simple protein/carbohydrate systems using mainly GROMACS and Amber force field. No ab initio or QM-MM simulations are intended for now. For instance, I have been working with a protein of approximately 1500 atoms in the presence of small carbohydrates (<100 atoms). For the protein alone, my home PC (i5-4570 CPU 3.20GHz, not GPU-accelerated) does approximately 5 ns/day, so I want something considerably faster than that.

Which hardware should I choose? Could you suggest low (800 US dollars) to high (2000 US dollars) price configurations with good power considering the current technology available? I am not sure if I need a GPU-accelerated machine, so I am open for different configurations.

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There is a recently published paper addressing the question of what is the optimal combination of hardware on which to run GROMACS:

Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L., & Grubmüller, H. (2015). Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry, (Spp 1648). doi:10.1002/jcc.24030

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I don't have experience with GROMACS, or even MD simulations, so take my analysis with a grain of salt, but GROMACS provides what appears to be a good analysis of their performance on different hardware configurations.

Of course the simulation time per day would depend highly on your molecular system, but they show speedups of 5x using a GTX Titan (the high end or above your price range) over a high end CPU and x3-x4 out of a GTX680 (I would consider this a consumer card, you can get GTX 700-series for a couple hundred dollars on newegg).

Depending on your exact budget you should be able to accelerate your computations by a factor of x3-x5 without too much trouble as long as you do your research on which GPU/CPU combination to buy. Just looking at their information, I would highly recommend going the GPU accelerated route.

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