[gmx-users] Arbitary small molecule for Martini force field

[XAvier Periole]

> I tried Martini force field and found it calculates with a good  
> result in appearance
> for a *specific* calculation prepared at the Martini website.
That is good to know :))
> Now, I wish to use another small molecule (such as lipid) for CG  
> simulation.
> Starting from the chemical structure, I draw it with MarvinSketch
> and save as pdb. After this I want to make a .gro file and .itp file
> which is compatible for Martini force field. Can u give me instruction
> for that?
you can find the main steps to build your own "martini" molecule in
a couple of papers. This is decribed in detail for lipids and amino-acid
in most recent papers:
Marrink et al J. Phys. Chem. B, 2007, 111 (27), pp 7812–7824
Montecelli et al J. Chem. Theory Comput., 2008, 4 (5), pp 819–834
> Or need  (or find if possible) experimental data to tune the
> parameter?
That you'll have to do yourself. You have to parameterize your molecule
to reproduce as much as possible data from atomistic simulations and
experiments.
> For my simulation the atomic simulation leads to
> segmentation fault (Memory: 2GB) and i feel the CG is necessary.
That is probably not related to the degree of desciption of your
system!
>
> Else if Martini is not useful for more general calculation,
it seems so ...
> let me know the alternative approach for CG calculation
> with GROMACS.
>
> taka
>
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