[gmx-users] very strange area/lipid value for POPC membrane system

[Justin Lemkul]

On 8/19/12 2:32 PM, Albert wrote:
> hello Justin:
>
>    thank you very much for kind reply.
>
>    My protein is so large (300 aa and 7 transmembrane helix) and it will
> definitely affect the lipids property. In this case, how can we know that the
> forcefield is good enough for protein/lipids modeling even people did lots
> microsecond simulation for the pure lipids itself (but as I saw that few people
> will did the test with such big protein inserted in a membrane)?
>

If the force field has been validated such that it reproduces pertinent 
properties of both the protein and the lipids, then that's the baseline for 
comparisons.  My comment was simply meant to imply that you shouldn't 
necessarily expect any given force field to produce realistic values, especially 
if you perturb the system by adding a protein.

The beauty of GridMAT-MD (if I do say so myself, in a very biased opinion ;) is 
that you get output of APL for each individual lipid, so you can get an idea of 
which lipids have what size and why.  If they are close to the protein, maybe 
they are tilting, compressing, or expanding due to hydrophobic mismatch.  Lipids 
further away that are less perturbed (or not at all) should, on average, have 
APL values comparable to bulk lipids.  We have done these types of analyses 
ourselves and have seen them done by others in published work.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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