VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri May 04 2018 - 11:06:12 CDT

I am really excited about the work you guys are doing to enable larger systems simulations. Also very impressed with the HIV that Dr. Schulten and his students did a few years ago.

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Friday, May 4, 2018 10:02:02 AM
To: McGuire, Kelly
Cc: Vermaas, Joshua; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: CellPack

HI,
  The new versions of VMD and NAMD have both seen heavy work to enable them
to simulate systems in the billion-atom range. While they run, it is
currently still hard going because every step of building such a massive
system is slow going. Just making VMD atom selections of typical complexity
on a billion atoms can take a few seconds!! You have to have a machine with
between 512GB and 1TB of RAM to to be able work on something in this size
range. Needless to say we're working on both tools to make modeling
and simulating complexes of that size practical. As Josh already pointed
out, all of this has to be paired with serious computing resources on the
back-end.

Best,
  John

On Fri, May 04, 2018 at 01:41:58AM +0000, McGuire, Kelly wrote:
> Wow, thanks for that. I did not see that page, very useful info there--_000_BY2PR01MB1816429E1371CD268B35A2E7FF860BY2PR01MB1816prod_--