[gmx-users] Martini FF....

[Justin Lemkul]

On 10/12/12 10:42 AM, rama david wrote:
> Hi Gromacs friends,
>
> I planed to use martini coarse grained ff to my simulation protocol.
>
> My simulation protocol is:
>
> I am placing two  peptide at far distance.IAt these point i am using Gromos
> FF they are initially in random coil structure.
> Now when I run the simulation for 100 ns they are coming close in
> antiparallel fashion.
>
>
> Now I am placing more than two peptide ( 30) .I am using martini FF ,
> I found that they are coming closer
>
> I have practical result they are also showing random coil peptide changing
> to the Beta sheet structure.
>
> But my Query for Martini is :
>
> As the martini ff is not representing the change in Secondary structure.
> That the Secondary structure is predefined therefore they are statics
> through out the simulation.
>
>
> Is it wise to say by martini, peptide  aggregate are beta sheet
> structure..????
>

I don't think you can make that assertion with any confidence.  I have limited 
experience with MARTINI, but it is for this very reason - the secondary 
structure limitations are significant.  The force field is great for well-folded 
proteins, but not for IDPs or amyloid systems.

> Another Query:
>
> Secondary structure are statics in simulation means that they are not
> changing at all in simulation. Alpha helix is going to remain alpha helix.
> or Secondary structure  can be change but we are not able to determine in
> which structure they will go.
>

No, the secondary structure is invariant.  There are actual bonds in the 
topology between backbone atoms that fix the structure.

-Justin

-- 
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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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