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

XAvier Periole 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  
> 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
> 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.
> taka
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090705/d4a8d920/attachment.html>

More information about the gromacs.org_gmx-users mailing list