[gmx-users] Hardware for GROMACS

[Raman Preet Singh]

Hello,


I am new to GROMACS and want to assemble a computer to run simulations of proteins and polymers (typically <50 kD). My questions are:

1. I plan to add two or three small-sized GPUs (768 CUDA cores/GPU) to the system. Is it OK to have a dual core processor or should I look for a processor with 6 or 8 cores?

2. GROMACS website (http://www.gromacs.org/GPU_acceleration) has a page on GPU acceleration and compares performance between different hardware combinations (6 core or 2*8 cores, with and without GPUs). It also mentions of "dodec + vsites(5fs)". I tried searching on Google but could not find what is "dodec+vsites(5fs)". Please help me understand these.

3. Apart from a good processor and 2-3 GPUs, is there any other hardware that I may require to accelerate the calculations. I am targeting simulations in time scales of a few hundred nanoseconds.

Thanks in advance for your help!


Regards,

Raman