Re: Why simulation running on linux is damn slow??

From: Natalia Ostrowska (
Date: Wed Nov 10 2021 - 09:02:01 CST

I have ran simulations of around this size on comparable setup and >20 days
is completely normal - use this time to do stuff that you will have to do
anyway, like writing analysis scripts etc. (applying for a grant at the
supercomputing center would be a good idea too :P)

Remember to download fragments of the trajectory every once in a while and
have a look at the system in vmd - so if something goes wrong you would
spot it as early as possible

Natalia Ostrowska
Univeristy of Warsaw, Poland
Centre of New Technologies
Biomolecular Machines Laboratory

wt., 9 lis 2021 o 02:33 Amir Zeb <> napisaƂ(a):

> Hello NAMD users,
> I have a system of ~250000 atoms and I want to run simulation for 100 ns.
> The time step is 2, so I put run = 50000000 in config file. It took 4 days
> and hardly completed 6400000 steps, this means it'll take >20 days to
> complete 100 ns simulation with this speed. The command I used is:
> namd2 +idle poll +p10 +devices 0 config.
> namd > xxx.log
> Details of my system:
> Linux, Ubuntu
> CPU(s) 40, online cups list 0-39, Core(s) per socket 10, Sockets 2,
> NVIDIA GM206 [GeForce GTX 960] (rev a1).
> but when I put the command nvidia-smi,
> it prints 'not found', but can be installed with: sudo aor install
> nvidia-340
> and many others.
> Please let me know what should I do to speed up the simulation?
> kind regards
> Amir

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