I have a basic student PC setup with 8GB RAM,1TB HDD, Intel i7 8th gen processor. I want to do a MD Simulation of a protein- ligand complex interaction of near about 500kda with 100-120 ns, I would be helpful if anyone suggest that whether it can be possible or not in this setup if possible suggest me some MD Simulation software for basic student computer.
I have a similar PC with 4 core Ryzen 3-3200G and an AMD GPU and Gromacs is able to deliver me a computing ability of 65+ ns/day. If you have a CUDA enabled NVIDIA GPU it would be pretty helpful for you in GROMACS to reach 120ns/day.
Hey Sohan! There are many MD codes which can fit with any computer architecture. One can use AMBER, CHARMM, GROMACS, NAMD or LAMMPS. I personally use GROMACS quite a lot and and runs fast on PC. It is also free of charge. You have mentioned the system which is 500 kda. It is large for a regular PC, but you can always try, since the duration of your simulation is about 100-120 ns.
Hi Sohan Seal ,
Try GROMACS (http://www.gromacs.org/), for this you need some basic knowledge of LINUX command line.
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