From: Ian Stokes-Rees (
Date: Wed Jul 21 2010 - 07:07:51 CDT

On 7/21/10 3:40 AM, Prskalo, Alen-Pilip wrote:
> I'm new in the VMD community, used Rasmol before. I am simulating
> systems of ~1.000.000 atoms in each frame and I intend to make nice
> videos later on. So it is obvious that I will have an enormous .pdb
> file containing large number of atoms AND frames to make the video
> look fluent. My question is: what is the best PC to do it? I do have a
> bit money on the side to upgrade my 4 Core, 4GB RAM PC, but how? First
> idea is of course to by extra RAM, to go to 8 GB or even 16 GB. What
> about the graphic card, presently I have only onboard graphics, would
> a good graphic card make the loading and rotation easier and if, how
> exactly (from the technical stand point).

I don't have direct experience with this, but from my indirect
experience you would probably be well suited to purchase one of the new
8 or 12 core per CPU AMD systems which can get you 32 or 48 cores in a
single box, include a recent nVidia CUDA 3.0 graphics card (a Tesla
would be best, but an OEM model would probably work alright as well),
and then buy at least 16 GB of RAM, if not more. From what I
understand, you can put in as many Tesla cards as your system can handle
and VMD will pick them up and use them all.

Are you running the simulation on the computer, or is the simulation
running on a separate MD cluster? If it is running somewhere else, you
could make do with fewer CPUs. If it is running on the new computer you
are going to get, you should aim for the 48 core AMD system. Here in
the US you can get such a system for about $7k, or "fully loaded" (fast
disks, lots of RAM, etc. etc.) for under $10k.

I am very interested to hear what other people recommend.