Hi Everyone,
I have just started to learn LAMMPS. I am working on lipid bilayers. I have checked some tutorials but still fail to understand from where to start for simulating a bilayer. Could I get some guidance?
Thanks & regards,
Sonika.
Hi Everyone,
I have just started to learn LAMMPS.
started to learn LAMMPS or started to learn MD. if it is the latter
case, then you are likely better off to start by reading text books
and bugging your adviser.
I am working on lipid bilayers.
are working or want to be?
I have checked some tutorials but still fail to understand from where to start for simulating a bilayer
what tutorials did you look at? and where exactly is your problem?
starting a bilayer simulation is not specifically different from *any*
molecular system. you generate some initial structure, assign a
topology with atom/bond/etc.types and then assign suitable force field
parameters. then you equilibrate and run you MD. in this respect
LAMMPS is not different from any other MD simulation program for
molecular systems. the physics remains the same, regardless of what
software you compute it with.
. Could I get some guidance?
this is really the task of your adviser or a more experienced member
of your lab. a mailing list makes for a bad replacement. moreover,
your question is far too generic to provide a specific answer, and you
won't find somebody here that has the time to be your personal
trainer.
axel.
Are you trying to simulate a coarse-grained bilayer, or a more
realistic all atom bilayer? What type of lipid, or lipid mixture do
you want to simulate? Do you plan to include cholesterol? (protein
inclusions?) If you plan to use a coarse-grained system, do you want
to use explicit or implicit water? (You could implement the Martini
force field in LAMMPS, for example.) Do you have a coarse-grained
model in mind (CMM?, Martini?, Cooke+Kremer+Deserno?,
Brannigan+Brown?)
I don't know how to build an all-atom simulation. However, LAMMPS is
still probably the most powerful, flexible program simulation program
you can use for building coarse-grained biomolecules. (..which I know
about... ESPResSo++ and OpenMM are also definitely worth
investigating.)
There is an example of how to build a coarse-grained lipid bilayer in
LAMMPS at www.moltemplate.org (scroll down to the bottom. That example
uses a slightly modified version of the model in this paper: J. Chem.
Phys. 135, 244701 (2011), and adds another lipid type and a protein
inclusion.) There is also an example using that same model to build a
vesicle (44000 lipids) at
tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/ in your
lammps directory. There is also a picture of it here:
http://www.ime.unicamp.br/~martinez/packmol/external.html
Once you are familiar with LAMMPS (and moltemplate), it should not be
difficult to modify these examples to work with any of the other
popular coarse-grained membrane models as well. (If you get stuck,
email me.)
There's also mbtools (for ESPResSo)
http://www.cmu.edu/biolphys/deserno/mbtools/mbtools_tutorial.pdf
Other useful free general tools:
topotools
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction
https://sites.google.com/site/akohlmey/news-and-announcements/sciencevsart
topotools
http://www.ime.unicamp.br/~martinez/packmol/
I hope this gives you a starting point. Good luck.
Andrew