Membranes: Difference between revisions
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The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. | The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. | ||
= References = | == References == | ||
<biblio> | <biblio> | ||
#Ulmschneider2005 pmid=15723347 | #Ulmschneider2005 pmid=15723347 | ||
</biblio> | </biblio> | ||
Revision as of 21:45, 27 June 2008
Simulations of proteins must also represent the environment faithfully (simulations in vacuum are not appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the solvent and, if it's a membrane protein, of the lipid bilayer. Here we discuss methods to represent the lipid membrane.
Explicit lipids
All atom
All atom representations include heavy atoms and all hydrogens. See united atom for the alternative.
United atom
A united atom representation combines carbons and aliphatic hydrogens into unified particles.
Implicit membrane
Dielectric slab
Statistical potential-based membrane
The membrane is parametrized based on the distribution of amino acids along the bilayer normal Ulmschneider2005.
References
<biblio>
- Ulmschneider2005 pmid=15723347
</biblio>
