Dear Experts
I need a list of specifications/components list for setting up a Desktop computer to do molecular dynamics simulation. The main purpose is to do Structure Based Drug Design and Vaccine design/Computational Chemistry Research (DFT analysis, HOMO-LUMO Calculation).
Target is to complete 700 Amino Acids-ligand (Phytochemical/peptide/vaccine construct) complex simulation for 100 ns / 200 ns in one day/One and a half day (36~40 hours).
Please suggest me which spec-based computer should I buy. Thank you very much.
Sheikh Sunzid Ahmed
Assalam o alaikum wa rahmatullahi wa barkatuhu
Hope you doing well
As per your requirement the desktop specifications should be 11th Generation Intel® Core™ i9 Processors
1 TB hard disk minimum
Graphic card GeForce GTX 16 Series
Waseem Ahmad Ansari Sir, Wa Alaikum Assalam Wa Rahmatullahi Wa Barakatuhu
Lots of thanks for your kind answer. Could you please let me know about the requirements of RAM for that purpose, and should I buy SSD instead of HDD 1tb. That might be more faster I guess.
For MD simulations and other compute-intensive tasks, it is helpful to have a CPU with a relatively high core/thread count and clock speed (frequency). Currently, one of the best CPU chips for high-end workstations is the AMD Threadripper Pro 5975wx, which has 32 cores/64 threads, a base frequency of 3.6GHz, and a turbo-boost frequency of 4.5GHz. This should be paired with 1-4 graphics cards capable of substantial acceleration via GPU computing (either OpenCL or CUDA). Among the best GPU accelerator cards are the Nvidia RTX 4090 and Nvidia RTX A6000 or RTX 6000 Ada. Recommended CPU memory is 64 - 512GB 3200 MHz RAM. The boot disk should be an M.2 1-2TB SSD. For fast read-write speeds of data, there are data-center class SSDs in the 2-16TB range with M.2 or U.2 interfaces. Longer-term data storage could consist of a NAS with spinning HDDs. All of this would not be cheap -- the computer would cost upwards of 20k USD and a few k more for the external NAS storage unit.
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