Re: the instance type selection for NAMD simulation in Amason marketplace

From: Ryan McGreevy (
Date: Mon Oct 15 2018 - 08:45:31 CDT

When the marketplace listing was created, g2 was a good candidate for
general use of VMD and NAMD on AWS while being relatively cheap. Currently,
for the best performance of NAMD specifically, you would want to look at
the newer gpu computing instances, p2 and the newest p3 types that have
more recent gpus in them. I don't believe we've benchmarked those instance
types, but a 30,000 atom system is not so big, so it should be doable on
AWS. You can always run the simulation for a short time to get the
benchmarking output to estimate the total time and cost.

On Mon, Oct 15, 2018, 8:16 AM sunyeping <> wrote:

> Dear All,
> I want to try to do NAMD simulation on cloud with EC2 of Amozon
> marketplace.
> From the webpage ( I
> learn that the NAMD and VMD vendor recommended EC2 instance type is
> g2.2xlarge, which is $0.65/hr. But I have no idea the performance of this
> instance for NAMD. I now have serval protein-water systems and each system
> contain around 3,0000 atoms. I want to do molecular dynamcis (MD)
> simulations on these systems with EC2 NAMD. I need to do 500 nanoseconds
> simulation on each of these systems. How many hours will it take using the
> g2.2xlarge? Is g2.2xlarge the fastest type for NAMD simulation or is there
> any other type which is faster and cheaper?
> Best regards Yeping Sun

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