VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Oct 31 2014 - 13:35:02 CDT

Hi Afroditi,

The quadro you listed is more than enough for running VMD. Personally
I've been quite happy going with the "gaming" cards. A GTX 980 or 970
will be cheaper with the same amount of RAM (which is the figure of
merit that determines the size of the system you can do the shiny new
things John was advertising yesterday with). For the ~100k atom systems
I work with frequently, I've noticed no problems with either my old GTX
580 or my newer 980 in driving a modest multi-monitor setup. In fact, I
might suggest you better invest the price difference in some combination
of more disk/RAM/CPU. This is mostly explained the features you are
actually buying when you get a quadro:

1.) A single slot form factor, so you can use the adjacent PCI slot on
the motherboard. Usually ignoreable, because most of the motherboards
I've seen have their fast PCI express lanes separated in such a way that
you are only blocking a "slow" PCI slot you wouldn't put a GPU on anyway.
2.) Lower power requirements. The quadros tend to have lower power draws
relative to their gaming card counterparts, which means you can get away
with a smaller power supply. You are buying/building the system from
scratch, and can match the power-supply size accordingly.
3.) Error correcting memory. Useless for VMD purposes as far as I can
tell. For running MD simulations themselves, useless as well, and may
actually be harmful. See http://dx.doi.org/10.1145/2484762.2484774 for a
comparison study that some of the Amber guys did in collaboration with
NVIDIA.
4.) The Quadros/Teslas usually have better double-precision performance
relative to the gaming counterparts (often by a substantial
multiplicative factor). This isn't helpful to you though, since the
developers of the MD packages with the largest "marketshare" for
biomolecular simulation (NAMD, Amber, Gromacs) use single-precision in
their GPU versions for the calculations.
5.) Better support contracts (ie, they exist). This is a big reason why
large corporations/government agencies buy them. Not sure if that is
something that is a factor at a single-user level though.

Or for those that prefer a short video explanation (aimed at gamers):
https://www.youtube.com/watch?v=U5Npt1BSF04

Basically you shouldn't have a problem with the card you selected, but
there may be a better fit for you in the product line.

-Josh Vermaas

On 10/31/2014 10:38 AM, Dudo wrote:
> well, the card costs only some thousand bucks so I am afraid in order
> to take full advantage of it you'll have to buy like 100 inch double
> full HD monitor or so, which does not come with the price :-(
>
> best,
> Dudo
>
> On Fri, Oct 31, 2014 at 3:46 PM, Afroditi Maria Zaki
> <afroditimaria.zaki_at_postgrad.manchester.ac.uk
> <mailto:afroditimaria.zaki_at_postgrad.manchester.ac.uk>> wrote:
>
> Hi!
>
> I am working on molecular dynamics and I am planning to buy a new
> workstation . The graphics card I am thinking of buying is Nvidia
> Quadro K4200 4GB, so I would appreciate your opinion whether this
> one is suitable for running VMD.
> Thanks in advance for your consideration!
>
> Regards,
> Afroditi
>
>
>
>
> --
> ____________________
> Ing. Dusan Racko, PhD
> https://www.researchgate.net/profile/Dusan_Racko
> Polymer Institute of the Slovak Academy of Sciences
> Dubravska cesta 3
> 845 41 Bratislava, Slovak Republic
> tel: +421 2 3229 4321