Fwd: vmd-l: MOE discussion

From: Mike McCallum (mmccallum_at_pacific.edu)
Date: Wed Apr 28 2004 - 23:11:43 CDT

What got me looking at MOE was this:


Perhaps this is more the NAMD group than VMD group (I don't know how
connected you are over there). The thing that attracted me to MOE was
the apparent ability and ease to (at least help) configure new
parameters for the charmm FF (then onto better things like NAMD2).
This implicitly means small structures, as it is usually enough to use
some small fragment of a larger whole to get the charges, radii and
angles for charmm.

It is very slick, but as I have not explored it in great detail, I'm
not sure it's $2k per year slick.

Cross-posted to NAMD-L.



Begin forwarded message:

> From: John Stone <johns_at_ks.uiuc.edu>
> Date: April 28, 2004 15:03:31 PDT
> To: Mike McCallum <mmccallum_at_pacific.edu>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: MOE discussion
> 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
> --
> 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

C. Michael McCallum                         
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax

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