VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 23 2015 - 13:37:27 CDT

Hi,
  SSDs can give a huge performance benefit to MD trajectory processing.
I wrote a paper in 2011 that describes this in some detail, where I
got VMD to read trajectories at several gigabytes per second using
multiple SSDs in a RAID:
  http://dx.doi.org/10.1007/978-3-642-24031-7_1

The performance does depend somewhat on the trajectory file format,
and my paper describes those issues in some detail also.

Cheers,
  John

On Wed, Sep 23, 2015 at 11:22:06AM -0700, Gianluca Interlandi wrote:
> Dear all,
>
> Does anybody have experience using a SSD or combined mechanical/SSD drive
> for reading large trajectories into VMD? Do any of the two provide a speed
> up compared to conventional hard disks? Also, how well are SSD/SSHD
> supported in Linux?
>
> I was considering ordering a Samsung Evo 850 Pro until I read some
> negative reports, e.g.,
>
> https://www.reddit.com/r/buildapc/comments/3a58s0/dont_use_linux_on_samsung_ssds/
>
> Thanks,
>
> Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> ----------------------------------------------------- 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/