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
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
