[gmx-users] any alternative methods?

[Justin Lemkul]

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

> thanks again for comments
> Albert
>
>
>
> On 08/22/2012 03:16 PM, Justin Lemkul wrote:
>>
>>
>> On 8/22/12 9:12 AM, Albert wrote:
>>> hello Justin:
>>>
>>>   thanks for reply.
>>>   I've read both the paper and manual script. As indicated from the output, I
>>> found the following line:
>>>
>>> 368    4.295    3.8840018217
>>>
>>> I just wondering how could it possible fro residue 368 with a value of 3.88?
>>>
>>
>> My guess would be that this particular lipid is probably bound very tightly to
>> some protein residue, which leads to the protein and lipid both contributing
>> to the lateral area in that region. In this case, the protein contributes more
>> area than the lipid does.  You should look at the coordinate file and see what
>> this residue is doing.
>

-- 
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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

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