George, > I am attempting to simulate lipid cubic phase using Coarse grained MD > from the spontaneous aggregation approach, starting from random mixture > of lipids in solution, in the spirit of JACS 2009 paper from the > Martini > community. I had several technical issues before setting up the > simulations and I would appreciate expert opinion on these.
I can't comment in terms of the coarse grain type of MD, as we are performing united atom simulations of phase behaviour, but the principles are still the same. > My main concern is about the interplay between the number of lipids in > the system, initial size of the simulation cell and the pressure > coupling method to use. What should be the recipe for choosing the > initial number of lipids? Obviously, I would think that one has to > choose the number large enough to form at least one unit cell of the > bi-continuous cubic phase. But what happens if I don't choose exactly > this "magic" number, but slightly more? Then I would think that after > running the simulation, the simulation box would contain more than just > a unit cell of the cubic phase. Can this be a problem? It is good that you are concerned, as it does influence the result. If you have sufficient size / number of molecules to form a non-integer number of unit cells, then the final structure will be distorted from what you would expect as the end result. The only way to get beyond this is have the system large enough that it is not an issue, and computational speeds are not at this level as of yet. You have a number of options available. Put in the "correct" number or dimensions, but you are constraining the results of the simulation, you might as well preassemble it, since you aren't actually allowing it to spontaneously form a structure, you are guiding it. Acknowledge that the structure formed may not be perfect and will have flaws in it, due to the dimensional issue, and simply work that into your work. > Also does the initial size of the simulation box matter if one > simulates > spontaneous aggregation process as long as the molecules initially > "fit" > into the box? If you are going for spontaneous aggregation, then random distribution of the molecules within the box is what you should be starting from. > And finally, what role should isotropic vs anisotropic pressure > coupling > play in such approach? Which pressure coupling method should be > preferred in such spontaneous aggregation simulation? We played with this for quite some time. In a perfect world, it would be best to using anisotropic pressure coupling, so you do not constrain the structure that is formed. However, in the world of MDS, it is simply not possible. You encounter major issues with simulation stability, the way the pressure coupling and alternating charges across one dimension of the box interact means that eventually you will end up with the box distorting to the point that you end up with a match stick or a pancake. We even played with adding various tweaks to the coupling algorithms that increase the resistance to changes in the box dimensions as they deviate from cube or get too close to the point at which it will explode. The algorithms works great. But you get back to the same point again, ultimately you are constraining the end result. And the flow on effects of that are harder to quantify than simply staying with isotropic. We are putting together a publication on the phase behaviour stuff we have done, some mention will be made of these issues in that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
