NAMD Build

[TBickle]

1) What will you be doing with this PC? Gaming? Photoshop? Web browsing? etc
Running molecular simulations using NAMD, data analysis, and other scientific applications.
2) What's your budget? Are tax and shipping included?
$2000
3) Which country do you live in? If the U.S, please tell us the state and city if possible.
Baltimore, MD
4) What exact parts do you need for that budget? CPU, RAM, case, etc. The word "Everything" is not a valid answer. Please list out all the parts you'll need.
Case, CPU, RAM, PSU, Video Card, Mobo, HD
5) If reusing any parts, what parts will you be reusing? Please be especially specific about the power supply. List make and model.
None
6) Will you be overclocking?
Yes
7) What is the max resolution of your monitor? What size is it?
2xZR2740w (2560x1400)
8) When do you plan on building/buying the PC?
Next Month
9) What features do you need in a motherboard? RAID? Firewire? Crossfire or SLI support? USB 3.0? SATA 6Gb/s? eSATA? Onboard video (as a backup or main GPU)? UEFI? etc.
May need SLI support depending on how NAMD interacts with multiple GPUs, everything else is extraneous.
10) Do you already have a legit and reusable/transferable OS key/license? If yes, what OS? Is it 32bit or 64bit?
Win 7 Pro, with VMs into Darwin

If anyone has experience running this kind of machine, how powerful and how many gpus do you normally run. Most of the data I've seen shows that only one GPU is in use for the simulations, and even then only minimally.

 

[tiraides]

I'm not very familiar with NAMD... overall, are all of your tasks more CPU-dependent or GPU-dependent?

Which type of GPUs (gaming or workstation) are generally used for your simulations?

Are you able to reach the Rockville, MD Micro Center store?

Which part of next month were you planning on buying everything?

 

[TBickle]

Are all of your tasks more CPU-dependent or GPU-dependent?
From the research I've done most of the time is still CPU dependent, although the GPU significantly speeds it up.
Which type of GPUs (gaming or workstation) are generally used for your simulations?
That's something I was hoping I could get some help with here. I've seen these simulations being run on mobile gpus, but most of the commercial workstations (Dell, HP, etc.) use workstation level graphics cards. I'm not sure of the need for the workstation graphics cards, since most of these jobs are going to be fairly interactive and their results will not be published. Our plan is to do the beginning things like selecting transition paths, reaction coordinates, etc, on this machine, and then put them on a cluster for the "real" calculations.
Are you able to reach the Rockville, MD Micro Center store?
Yes.
Which part of next month were you planning on buying everything?
04/13/12

 

[Dangman]

Are you able to reach the Rockville, MD Micro Center store?
Yes.
Which part of next month were you planning on buying everything?
04/13/12

In that case, please come back around April 3rd or 4th and bump up this thread as by then we will know what CPU and motherboard deals Microcenter will have around that time frame. Unfortunately, MC deals change every month so a MC setup we recommend today may not be the same setup we recommend in a month.

Though I'll be honest: I'm not familiar with NAMD either. With that said, from the limited research I've done, NAMD can use multiple GPUs. From the NAMD mailing list:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/2447.html

So something like two GTX 560 Ti 448 Cores or GTX 570 cards would be your best bet. A good 750W PSU like the Corsair TX750 V2 should be enough power.