[gmx-users] Martini FF....

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 16:55:47 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list