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

[Albert]

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)?

thank you very much
best
Albert


On 08/19/2012 08:14 PM, Justin Lemkul wrote:
> If you tell GridMAT-MD that there is no protein, it will assign the 
> "empty" space to lipids, leaving you with an inflated value, because 
> area grid points that are supposed to belong to the protein are 
> erroneously assigned.
>
> As for why the average APL values do not match the literature, that's 
> a question of force field, .mdp file, simulation length and sampling, 
> and what effect your protein might have on the surrounding lipids.  
> Values for pure lipids are not necessarily comparable to those of 
> protein-containing systems if the protein affects lipid structure and 
> dynamics.
>
> -Justin