On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: > > > On 10/18/12 2:43 PM, klexa wrote: > > Hi Gromacs users, > > > > I think I am a bit confused about the proper way to handle boxes that are > > not > > standard cubes. I'm trying to run a membrane simulation where a cyclic > > undecapeptide is inserted into the membrane and I want the water layer to be > > sufficiently thick that if it were pulled, the peptide could be fully > > solvated > > by the water. To avoid having an enormous box of membrane and water, I have > > an > > orthorhombic box containing my peptide and bilayer. It minimizes alright > > with > > Gromacs, but when I go to equilibrate it it fails because it's too skewed > > to be > > a triclinic box. I've tried modifying the box with editconf and converting > > it to > > a rhombic dodecahedron, sort of like the manual suggests for a membrane > > system. > > I'm not sure that even that is sensible since it seems like I would be > > losing > > content that way, yet nothing is clipped, and I did this after using > > trjconv to > > remove any periodicity from my prior simulation of this system (in Desmond) > > but > > doing so gives me a starting potential energy of NaN for the new system > > that I > > obviously cannot work around. Is what I am trying to do even possible? If > > it is, > > it seems like there is probably a better way than the way I chose, so if you > > have any suggestions, I would be greatly appreciative. > > > > I have never produced a membrane system with a hexagonal cross-section like > the > manual describes. The most straightforward approach in my mind is simply a > rectangular box. It will save you a ton of headaches. > > > I'm trying to run this simulation with AMBER FF99SB parameters for the > > peptide, > > Tieleman's lipid parameters for POPC, and SPCE waters, so just as a sanity > > check, is it reasonable to consider a system like that? > > > > I don't know how this would even run. The AMBER protein force field and > Berger > lipid paramters use different combination rules, and I have never seen a > demonstration that one can use them together. It is most straightforward to > use > a Gromos force field or OPLS-AA with modifications to account for the changes > in > combination rules.
Or just use a self-consistent FF and setup already published/validated for such a system, like AMBER+GAFF or CHARMM+CGENFF. The choice of forcefield combinations for a peptide-membrane system doesn't require completely reinventing the wheel these days. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
