[gmx-users] any alternative methods?

[Albert]

On 08/22/2012 03:58 PM, Justin Lemkul wrote:
>
>
> On 8/22/12 9:54 AM, Albert wrote:
>> hello Justin:
>>
>>   thanks for reply.
>>    I've checked this residue, it is close to protein but I am still 
>> curious for
>> the value with 3.88. Even we also observe something 11, 13 which are 
>> the same
>> weired to me. here is the screen shot for this residue.
>>
>> https://dl.dropbox.com/u/56271062/1.jpg
>>
>
> I can't tell anything from this angle.  Lipids will sample 
> configurations that lead to their expansion and contraction within the 
> bilayer plane over time.  An individual lipid in a single snapshot 
> simply represents one possible value within a distribution of values 
> that might be observed.  Other lipids and molecules near the interface 
> will affect its individual APL.
>
> -Justin

hello Justin:

   I think I found similar case which was report in g_membed paper by 
GERRIT GROENHOF. This paper was released on J Comput Chem 31: 2169–2174, 
2010 titled "g_membed: Efficient Insertion of a Membrane Protein into an 
Equilibrated Lipid Bilayer with Minimal Perturbation"

in figure 3 of above paper, Gerrit showed that the ALP of POPC is do 
something around 54. here you can find the figure

https://dl.dropbox.com/u/56271062/figure3.jpeg

It is also comment that the software for ALP calculation overestimate 
the area of protein so that the value is far from pure lipids ALP. The 
author also state that the protein itself may also influence lipids 
property.


best
Albert