[gmx-users] Arbitary small molecule for Martini force field
takayama at ceres.ocn.ne.jp
Sun Jul 5 04:31:19 CEST 2009
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
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