AMBER Archive (2009)
Subject: RE: [AMBER] Computational Resources
From: Ross Walker (ross_at_rosswalker.co.uk)
> One time, I read AMBER has a limit for computational resources, it
This is a very complicated question that depends on a huge number of factors, not least the specific problem size and type of run you are doing, whether you are using sander or pmemd, what your hardware is, what the interconnect is etc etc.
In short if you can you should be using PMEMD. This will perform much better than sander and will scale a lot further. If you are running replica exchange then generally you can run a lot more processors (in sander) than you would for a standard MD run. Your best bet is to take the system you want to run on the machine you plan to use a run some short benchmarks to check performance and scaling.
For reference you can take a look at:
For the U.S. TeraGrid supercomputers see:
These timings are all for standard (PME) MD runs using PMEMD v10.0.
All the best
Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.