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

[Justin Lemkul]

On 8/19/12 12:16 PM, Albert wrote:
> Dear All:
>
>   I am using GridMAT-MD to calculate the area/lipid for my POPC system. The
> whole system was consist of a 300aa protein, 116 POPC and 0.15M NaCl.
>
>
> 1. I calculate the area/lipids by GridMAT-MD with the protein in it and I got a
> value:
>
> Ave APL = 54.1013569676733 sq. Ang
>
> 2. I removed the protein and I get another value:
>
> Ave APL = 76.1121752016697 sq. Ang
>
> Do you have any idea what happen for my calculation?  Of course I truned the
> line "protein    yes/no" for case with/without protein in the example param
> file. What need to mention is that both values are far from the POPC real
> area/lipids which should be something around 64.
>
> Does anybody knows what happen?
>

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

-- 
========================================

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

========================================