[gmx-users] Martini FF....

rama david ramadavidgroup at gmail.com
Fri Oct 12 16:42:15 CEST 2012

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

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.

Thank you in advance,

With best wishes and regards.
Rama david

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