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
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