Re: a philosophical question...

Date: Mon Feb 19 2007 - 20:57:31 CST


I'm sorry I missed your earlier posting on this subject.

I think the problem with lipids is that our field is still experiencing growing pains, since we're limited by the computational power. Realistically, we're still simulating micro- ensembles (such as NVE, NPE), but the intersection between different molecular components requires a larger approach to these systems. I do think our field is evolving, but the timescale is far different than a postdoc's lifespan. 

I believe that the dysfunction between academia and industry is due more to the immature state of our field rather than any misaprehension of ability or interest, although if anyone has any evidence to the contrary I am ALL ears 8~).

Dan Strahs

----- Original Message -----
From: Richard Wood <>
Date: Monday, February 19, 2007 9:20 pm
Subject: Re: namd-l: a philosophical question...

> You wrote, "If we don't do more simulations of mixed bilayers,
> it is certainly not because of
> the capabilities of such or such VMD plugin, it is because we
> mostly don't  know how to simulate them properly."  If
> this is the case, how can we simulate ion channels or protein-
> lipid systems "properly"?
> I mentioned the VMD plug-in because people seem to rely on these
> programs with their plug-ins to build various things; in the
> case of NAMD, it's lipid bilayers.  It seems to me that one
> could build an unsturated lipid as a pdb file and then create
> the proper topologies and
> go from there, much like we do with proteins (proteins aren't
> built using a "neat" plug-in).
> Do I get the sense that people think that "different" problems
> should be handled "differently"?  It's kind of like being
> told a "simulation isn't a simulation, it depends on the
> conditions...".  Maybe this is why our field is
> dysfunctional as far as the gap between academia and industry?
> Richard
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> ----- Original Message ----
> From: Jerome Henin <>
> To: Richard Wood <>
> Cc:
> Sent: Monday, February 19, 2007 7:09:49 PM
> Subject: Re: namd-l: a philosophical question...
> On Monday 19 February 2007 18:16, Richard Wood wrote:
> > As far as someone commenting to me, "do you have any philosophical
> > questions about MD?", I would say that I do.  In fact, I
> have many.  Here
> > is one.  I have noticed that several (many?) people are
> working in the
> > field of lipid simulations,  in the hope of learning
> something about cell
> > membrane behavior.  I am wondering if any of these people
> take into account
> > the fact that a cell membrane is not made up of a single type
> of lipid, but
> > generally more than one, and that some of these lipids are
> unsaturated (to
> > assure that the membrane won't freeze).  I would like to
> know how this is
> > handled.  The membrane building tool of VMD won't allow
> the building of a
> > mixed lipid bilayer.  How does one get around this?
> By carefully navigating around tricky questions and mined areas.
> Lipid
> bilayers are just very, very difficult systems, be it for
> experimental or
> computational studies (and the two are completely linked). What
> we are in now
> is a kind of middle-age of lipid simulations, if I may
> paraphrase KS. If we
> don't do more simulations of mixed bilayers, it is certainly not
> because of
> the capabilities of such or such VMD plugin, it is because we
> mostly don't
> know how to simulate them properly. Actually, even our models of
> most
> single-component bilayers are pretty unreliable.
> That's why most people prefer to ignore lipid-specific problems
> and just treat
> them as "whatever greasy thing my protein is embedded in". I
> suppose it is
> okay most of the time.
> Jerome
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