[gmx-users] very strange area/lipid value for POPC membrane system
mailmd2011 at gmail.com
Sun Aug 19 20:32:48 CEST 2012
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
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
More information about the gromacs.org_gmx-users