Re: running simulations on different machines with different versions of NAMD

From: Aron Broom (
Date: Fri Jun 15 2012 - 05:38:20 CDT

I may be off base here as I don't know the details of what you are doing,
but protein folding/unfolding has an astounding number of degrees of
freedom. So unless you are looking at a fairly short peptide, I wouldn't
expect the same pattern to reproduce itself very often, regardless of
simulation software or hardware.


On Fri, Jun 15, 2012 at 2:29 AM, Puspita Halder <> wrote:

> Dear All,
> I was doing high temperature protein unfolding simulations in our
> CPU-based i686 GNU/LINUX machine by using NAMD_2.7_LINUX-x86 version for
> the last few months. Recently, we are using GPU-based x86_64 GNU/LINUX
> workstation in our lab for running the similat type of simulations using
> NAMD_2.9_Linux-x86_64-multicore-CUDA version.
> My question is : should I expect different extent/pattern of unfolding by
> running the same simulation in these two different computer systems? If so,
> what is the reason behind it? Should I use the same machine for the entire
> unfolding simulations?
> Thanks for your help in advance.
> Puspita

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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