[gmx-users] Simulation of ordered molecular structures

[Justin A. Lemkul]

Quoting Peyman Yamin <Peyman.Yamin at cbi.uni-erlangen.de>:

> Dear gromacs users,
>
> I'm trying to simulate amphiphilic molecules, building stable
> structures by non-bonded interactions. I have seen in biological research,
> membranes and proteins therein are often subject of simulations. A cell
> membrane, I guess, could be an example of a structure built not by hard-core
> chemical bonds.
>
> Let's say you know experimentally that molecule X, builds starlike
> structures! Or a surfactant builds a sphere. Now to simulate this - to see
> e.g. the diffusion of other molecules in and out - does it make sense to
> build a sphere of, say 100 - the number you may know again from experiments -
> in a spherical geometry, and let them deal with eachother by a forcefield,
> or it's necessary to explicitly fix their positions?  If yes, will it give
> realistic results? In the end one could fix positions of 10, 100 and 1000
> molecules as a sphere, though only those with 100 are stable, in lab!

In theory, you can fix anything to any set of points, but whether that's
meaningful or not is questionable.  Now, position restraints are typically a
part of a thorough equilibration scheme, but I don't see any point in trying to
generate data of a micelle that you've artificially induced to stay together. 
Whether or not it's stable is dependent upon the parameters you've chosen for
the molecule of interest (not always an easy task, they may have to be
derived).

One can start with a pre-arranged micelle, star, or whatever, and check for
stability, or one can start from an arbitrary starting configuration and see
self-assembly.  I've seen reports of such behavior for micelles and bilayers. 
Whether or not this behavior is feasible is dependent upon having a set of
well-derived parameters for your molecule of interest.

-Justin
>
> I would greatly appreciate any comment, from those who do membranes or
> other alike predefined structures.
>
> Thanks in advance,
> Peyman
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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