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

H T takayama at ceres.ocn.ne.jp
Sun Jul 5 04:31:19 CEST 2009

Dear all,

I tried Martini force field and found it calculates with a good result in 
for a *specific* calculation prepared at the Martini website.

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? Or need  (or find if possible) experimental data to tune the
parameter? For my simulation the atomic simulation leads to
segmentation fault (Memory: 2GB) and i feel the CG is necessary.

Else if Martini is not useful for more general calculation,
let me know the alternative approach for CG calculation

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090705/00e8d454/attachment.html>

More information about the gromacs.org_gmx-users mailing list