[gmx-users] Arbitary small molecule for Martini force field
x.periole at rug.nl
Sun Jul 5 13:14:51 CEST 2009
> 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
> 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
That you'll have to do yourself. You have to parameterize your molecule
to reproduce as much as possible data from atomistic simulations and
> 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
> Else if Martini is not useful for more general calculation,
it seems so ...
> let me know the alternative approach for CG calculation
> with GROMACS.
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