VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 28 2004 - 17:03:31 CDT

Mike,
  I don't have much personal experience with MOE.
As you can imagine I'm swamped working on VMD nevertheless doing
much of anything else. :)

Others have told me that MOE does a good job with small structures, but
becomes unusable when working with large structures. That's its main
weakness from what I understand. As you can imagine, many tools offer
varying degrees of similar functionality, but they typically specialize
in a particular niche. The niche that VMD, NAMD, and psfgen fill is
in working with very large structures, running on parallel computers,
and analyzing large molecular dynamics datasets. Other mature
commercial tools do some or all of what VMD/NAMD do, but for small
structures, and some have easier-to-use GUIs for structure building,
but the packages I'm personally familiar with self-destruct when
working with huge structures/simulation trajectories, etc.

There will always be room for more viz/sim codes that specialize in
a particular area, no single tool/toolset does everything perfectly.
Its a lot easier to design software that performs a small number of
tasks every well than one that attempts to be everything to everyone.
VMD and NAMD are well suited for their particular problem domain but
it is inevitable that other packages are better at things they specialize
in. MOE is good at a number of things that VMD/NAMD/psfgen don't
really do at all. Similarly, you'll find that even among the free
viz/sim tools, each one has its own strengths and weaknesses.

Always use the right tool for the job.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 28, 2004 at 12:43:22PM -0700, Mike McCallum wrote:
>
> Because of the tutorials at the ks.uiuc.edu website, I have been
> introduced to MOE (http://www.chemcomp.com), and am playing with an
> evaluation copy of it. It seems to be a great package, particularly in
> helping integrate perhaps the most tedious chore in simulations --- new
> parameter generation. However, it is quite expensive, and has a yearly
> license, which of course is infinitely more costly than what I (most of
> us?) are used to (Charmm, G03, VMD, NAMD, AMBER, etc etc). It appears
> much more convenient to use, though it does duplicate much of what the
> VMD/PSFGEN/NAMD combination does.
>
> Have other people been using this package? What do you think? John
> and Justin, I'm particularly interested in what you have to say, as you
> all appear to have some experience with it.
>
> Cheers
> --
> C. Michael McCallum
> http://chem.cop.uop.edu/cmmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> (209) 946-2607 fax
>
>
> --
> C. Michael McCallum
> http://chem.cop.uop.edu/cmmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> (209) 946-2607 fax 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078