Dear All,
Has anyone simulated artificial synthesis of phospholipid vesicles using LAMMPS. What would be an ideal visualization software for the same?
Regards,
Amrita
Dear All,
Has anyone simulated artificial synthesis of phospholipid vesicles using
what do you mean by "artificial synthesis"?
wouldn't it be better to do a literature search for this? you are much
more likely to find, if somebody has done something like what you are
looking for or something similar. the specific choice of MD code is
rarely crucial for a study, unless it is the only MD code providing an
implementation for a particular potential or method.
LAMMPS. What would be an ideal visualization software for the same?
that is impossible to say. there are quite a few (molecular)
visualization software packages around and what is good or bad is
often a question of personal taste and technical expertise.
axel.
If it helps, here is an example of how build a (coarse-grained)
phospholipid vesicle:
http://www.moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010.html
For more pictures and a complete list of input files, visit this page
http://www.moltemplate.org
and scroll down...
This particular example uses PACKMOL to generate the atom coordinates,
MOLTEMPLATE to construct the data & input-script files, and
VMD+TOPOTOOLS to visualize the vesicle. There are other ways to build
this kind of system. It depends on which tools you are familiar with.
If you want to add solvent molecules inside and outside the spherical
shell, you can do that using PACKMOL as well.
You probably don't want the protein inclusions, so you can get rid of
the "1beadProtSci2010.lt," file, and delete everything below this line
in the "system.lt" file:
# -------- interactions between protein and lipids ----------
http://www.moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
--- Customizing the .lt files ---
The lipids are defined as molecule-objects named "DPPC" and "DLPC" in
the "CGLipidBr2005.lt" file.
http://www.moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
These are coarse-grained molecules with only 5-atoms and 4-atoms,
respectively. Replace them with the molecules of your choice. You
don't have to embed them in the same .lt file. You can make separate
.lt files for each lipid type, if you prefer.
However you need to specify the atom-types, masses, coordinates, and a
list of bonds in the molecule. If you are willing to use OPLSAA
force-field, then you do not need to manually specify the force-field
parameters or atom partial-charges. (Moltemplate will generate them
for you. Refer to the OPLSAA examples in the "examples/all_atom"
subdirectory for more information.) Otherwise, you do.
--- alternate method ---
If you already have a DATA file (LAMMPS format) and an input script
which describes the lipid molecules you want to use (topology and
force-field information), then you can convert this molecule to an
".lt" file (which you can use as a substitute for the
"CGLipidBr2005.lt" file in this example). You can do this using a
utility called "ltemplify.py" (also downloadable at moltemplate.org).
This way you can avoid building your own .lt file from scratch.
A final note about PACKMOL
PACKMOL is a great program, but it can be tricky to get high uniform
packing-density for large vesicles. It may take a few tries.
--- XYZ files also needed ---
In this example, the atom coordinates for a lipid molecule are also
stored in separate files: "DPPC.xyz" and "DLPC.xyz". You need to
update those as well:
www.moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz
www.moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz
--- details ----
You need external .XYZ files in this case because for this example,
I rely on PACKMOL to construct the final atomic coordinates, and
PACKMOL knows how to read .xyz files. (Otherwise, you don't need to
make XYZ files.) Make sure the atom coordinates in the XYZ files are
listed in the same order they appear in the "Data Atoms" section of
the ".lt" file which defines your lipid molecule-objects.
I hope this helps.
Andrew