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

[Justin A. Lemkul]

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

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