[gmx-users] Hard Drive Speed

[Erik Lindahl]

On Wed, 2002-05-22 at 11:13, Donald E. Elmore wrote:
> Hi all--
> 
> I was just wondering if anyone could give me an idea how important hard
> drive speed is for overall simulation speed.  More specifically, I was
> curious how much slower a run would be if it were storing trajectory files
> (.trr, .xtc, .edr) to an hard drive (7200 RPM) versus a SCSI
> hard drive (10,000 or 15,000 RPM).
> 
> Thanks!
> 
> -Don Elmore
> 

Hi Don,

Unless you store your coordinates extremely dense (like every step or
every 10 steps) it shouldn't have any effect at all.

Most people here use "El cheapo" IDE drives since we really need the
storage capacity. If you're only going to use the drive for data storage
(in contrast to swap/OS partition) you would even be fine with 5400 rpm.

Note that the edr file format is quite intelligent - even if you only
write to the energy file say every 1000 steps, you will still get the
*true* (based on every single step) averages & fluctuations when you do
analysis.

If you really need to store the coordinates every single step or so you
might want to go SCSI, but those trajectories will be huge. (Although
you can make the xtc files smaller by only writing e.g. the protein).

Cheers,

Erik