I am trying to buy a computer for molecular dynamic studies performed by Gromacs. I have found this computer in the market ThinkPad P17 Mobile Workstation. Do you think it is not good enough to run a simulation for 16 kD protein with small ligand for 100 ns? if it is enough, how much time does this computer need to perform this simulation (an estimation) ?
16KD protein should be fine.
Considering that it is a 4 core processor , graphics has 768 cuda cores, and your protein is small, it should take around 1 -1.5 days .
I would say it is not fine. The ThinkPad products are workstations for post analysis and paper work. They are definitely not good for high performance computing. If you awnt to use MD packages then you need much more cores ~ 20 or some medium-quality GPU cards. The data output is also a problem for laptops. You'd better have a large disk, which is often not equipped or suitable for laptops. I personally recommend you to have more experience about high performance computing before buying something yourself.
I agree with Zhaoxi Sun
1TB of hard drive, which is typical of laptops, is not enough. You will need to add additional HDDs and laptops usually do not have the space to mount them.
Similarly, the machine should be able to run for hours/days. Although modern laptops are for sure well optimized, the heat is likely to be quite a problem.
Keep in mind that when you buy a laptop a lot of money is going into extras that you do not need in MD simulations, such as design/optimization of hardware and top quality screens. It is better to invest the money on a small workstation with good GPU and many CPUs, where you will have enough space for HDDs and heat control. Moreover, they are easily upgradable, if one need to add more RAM/change or add a HDD/change or add a GPU/change processor and so on, while this is basically impossible (and when possible uselessly expensive) on laptops.
About the simulation, it depends on a lot of things, especially on the number of atoms (all-atoms, coarse grained or what?), so basically on the forcefield and the time step you are going to use. With GROMACS2021.1 and CUDA, on a personal laptop with 12 cores and NVIDIA RTX 2070, I get more than 150ns per day with 30k atoms circa using CHARMM36 and 2fs time steps.
Rajesh Pal ，I would say that there are 16K atoms in protein alone . When the all- atom MD simulation needs to be solvated, the whole system is estimated to be tens of thousands of atoms. Most of the calculation cost of molecular dynamics simulation is spent on calculating solvents interactions. I feel that computing resources are not enough.
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