Tutorial for CMM lipids in LAMMPS

Sorry, forgot the CC the mailing list…

I was thinking something equivalent to the basic tutorial for NAMD (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html).

Going through the basic file requirements and commands/parameters needed to run the simulations.

I haven’t stared a simulation yet, I figured I read up on it a bit more before getting my hands dirty.

Jesper

Sorry, forgot the CC the mailing list...

I was thinking something equivalent to the basic tutorial for NAMD
(http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html).

Going through the basic file requirements and commands/parameters needed to
run the simulations.

using LAMMPS for molecular systems is conceptually similar to using NAMD.
so most of the tutorial would apply as well. what is different are the
file formats
(a data file replaces the .pdb/.psf combo) and names of commands.

LAMMPS supports more types of potentials and thus the data file format
is more flexible, which makes it difficult to write a generic tutorial. more
importantly, LAMMPS doesn't come with a tool to generate the data file
(for the same reason), so you'll have to come up with a way to build it or
convert a different input set. most people have their own scripts or tools.
some are in the tools directory. attempts to a more generic way of building
input decks are listed here: http://lammps.sandia.gov/build.html

I haven't stared a simulation yet, I figured I read up on it a bit more
before getting my hands dirty.

also check out the examples folder for how to build input scripts.
if you pick a suitable example and combine it with the generic
wisdom of how to set up a good MD of a bio system, you should
have a fairly smooth start.

HTH,
    axel.

There is a detailed tutorial how to build a coarse-grained lipid
bilayer mixture (based on a different published CG model developed by
my colleagues). There is also a tutorial how to insert a different
coarse-grained protein into this bilayer. These examples/tutorials
are at
http://www.moltemplate.org
(scroll down to the bottom of the page to see the lipid+protein example).

That particular lipid model is a simple 4-5-atom (3-atom-type) lipid
model. It uses tabular forces to approximate the 1/r^2 attractive
interaction between one of the head-group atom types.

I imagine that it would be pretty easy to adapt this example to use
the USER-CMM pair potentials. (It would also be faster because you
don't need tabulated potentials.) I would love it if you would like
to create a moltemplate version of the CMM coarse-grained lipid model
(or any other coarse-grained lipid model), and are willing to share
it. I would be happy to post it as an example for others to use.
Moltemplate should be compatible with almost any coarse-grained model
which lammps is capable of simulating. (That was its main goal, at
least.)

Andrew

Hopefully by tomorrow I will have a new and significantly
easier-to-use version of moltemplate available for download by
tomorrow. I'll post again soon when it is ready.

Thanks both Axel and Andrew for the feedback.
Andrew I'd be happy to write a tutorial if I end up using moltemplate successfully.

Best,
Jesper

Cool!
Let me know if you get stuck.

Andrew