[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Respected Sir,

Greetings from Pawan.
I read in the manual about the freeze-grps but dint find a good explanation
about the usage.
Can you please tell me how to use freeze-grps in all dimensions during the
minimizations ?

Thanking you,
Pawan

> On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>

> Pawan Kumar wrote:
>
>> Respected Sir,
>>
>> Thanks for all your help, suggestions and guidance.
>> I have few more queries.
>> Which type of box is appropriate in editconf - cubic or triclinic ?
>>
>
> That depends entirely upon the dimensions of your system and what is
> adequate to accommodate the size of your embedded protein.
>
>  I have read in one of your mails in the archives that POPE bilayer
>> contains some bad interactions. As it contains more no. of lipids (340) it
>> covers the full protein ( trimer which I am working on ) other than the few
>> loop regions. How far that bilayer can be used or is it fine to use the
>> biger bilayer of popc128a whcih I obtained by genconf ?
>>
>>
> The choice of lipid should not be based on a size convenience.  It should
> be based on a valid model system, and experimental evidence to which you can
> correlate your results, if possible.
>
> POPE presented a terrible challenge, since during the in vacuo InflateGRO
> minimizations, the headgroups folded in on themselves to form intra-molecule
> hydrogen bonds that resulted in a collapse of the molecule.  The solution
> was to use freeze-grps in all dimensions during these minimizations, and
> then equilibrate very carefully.
>
>
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> 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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>>
>>
>
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