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

[Pawan Kumar]

Respected Sir,

Thanks for your help and suggestions.
First I will try to use POPC (the one generated using genconf) . If it
doesnt work then I will switch over to POPE.
I will ask you if I have any further queries.

Thanking you,
Pawan


On Mon, Mar 23, 2009 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Pawan Kumar wrote:
>
>>
>> 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 ?
>>
>>
> If you search for "freezegrps" within the list archive (the "Search"
> feature of the Gromacs homepage), you will find several hundred results,
> many of which provide examples of what users are trying and what may or may
> not work.  This should be instructive.
>
> In a general sense, freezegrps are just like anything else under the group
> theory in Gromacs.  Make an index group for the group of atoms you want to
> freeze (i.e., headgroups) and the dimensions in which you want them frozen
> (x, y, z - yes(Y) or no(N) for each).
>
> If you are choosing the route of POPE, it is very difficult to get these
> systems built using InflateGRO.  At least, that has been my experience.
>  Prepare to spend a lot of time with trial and error and very careful
> equilibration.
>
> -Justin
>
>  Thanking you,
>> Pawan
>>
>>    On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul <jalemkul at vt.edu
>>    <mailto: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 <http://vt.edu> | (540) 231-9080
>>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>            ========================================
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>>
>>
>>
>>
> --
> ========================================
>
>
> 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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