[gmx-users] Re: Gromacs system requirements

Erik Lindahl lindahl at stanford.edu
Tue Jun 17 07:04:01 CEST 2003

Hi Jason,

It's best to post questions to the gmx-users list; it usually gets you 
a reply faster when I'm traveling, and the answers get archived so 
other users can search the list :-)

In general, Gromacs is very lean on memory and hard disk usage. A 
typical simulation will probably use 20-30 Mb, and unless you are 
saving every single frame you'll be happy with a cheap but large hard 
disk to save your trajectories. (256 Mb of ram and 5400 rpm is quite OK)

Spend your money on the CPUs. Intel Xeons (the SMP version of Pentium4) 
are really getting cheap now. If you want to go really cheap you can 
buy from a local noname-vendor and install Linux yourself, but the 
first time I'd recommend spending $50-100 extra and get a system from 
Dell or some other vendor with warranty & support.

Within a processor model (like Xeon) the performance is essentially 
proportional to the clock frequency, and you probably gain 10% from an 
800MHz bus instead of 533MHz. The "sweet spot" is usually somewhere in 
the middle field...



On Monday, June 16, 2003, at 09:44  PM, Jason Dorsey wrote:

> My name is Jason Dorsey.  I am a student at The University of Toledo 
> currently enrolled in their pharmacy program.  I was interested in 
> building our department a new workstation to runs Gromacs on for 
> molecular modeling.  Could you help me out by giving some hardware 
> requirements?  I was thinking a dual processor PIII 1.2, but how much 
> cache, 1 gig of RAM, but how fast, and do the hard drives need to be 
> special or will a normal 7200 do?  Also what type of graphics card 
> would be needed? 
> Our department is currently using a Silicon Graphics Indigo 2 machine 
> but it is slowing down as it gets older.  I really appreciate any 
> feedback you can give me.
> Thank you,
> Jason Dorsey
> "Failing to understand the consequences of our inventions while we are 
> in the rapture of discovery and innovation seems to be a common fault 
> of scientists and technologists"
> Bill Joy
> cofounder SunMicro
> http://www.wired.com/wired/archive/8.04/joy_pr.html

> MSN 8 helps ELIMINATE E-MAIL VIRUSES. Get 2 months FREE*.
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