Ok thanks My primary concern is to cancel membrane-protein drift - the protein getting pushed to one side of the membrane box (also it's important for me to have the protein stay centered in the box too). I have not seen stability issues otherwise with COM turned on in the case of the unbound protein and the membrane as separate COM groups. The only instability I have encountered thus far is LINCS crashing due to too much forces if I set the restraint forces too high (like 100000 kJ/mol), but I've resigned myself to the fact that the residual RMS drift appears acceptable at the end of membrane/solvent equilibration runs if I drop it down to 10000 kJ/mol during NPT equilibration).
On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote: > > > Peter C. Lai wrote: > > Should I couple a ligand associated with a membrane protein to the same > > COM group as the Protein_POPC group? It makes sense to me that would be the > > case since if we are investigating the interaction between protein+membrane > > and ligand we want to have the same COM correction vector applied to both > > relative to SOL_Ions but I just wanted to make sure... > > > > If specifying multiple groups for COM motion removal, yes, the intuitive > solution is to group the ligand with the protein (since they're physically > bound, presumably). The general complication is whether or not multiple COM > groups are necessary - if the protein protrudes out into the solvent in any > substantial way, you could have instability when the solvent and > protein/membrane COMs get re-set. I have seen this before in the case of a > protein in water with separate COM groups (which is not appropriate, for the > record). Membrane systems are somewhat more complicated because they form > interfaces that can slide, but if the protein somehow affects this behavior, > well, I don't know that there's a trivial solution other than "comm_grps = > System" to avoid possible instability. If you're interested in > diffusion-related properties, on the other hand, that may not be appropriate. > Plenty to think about, but again, probably no "easy" solution. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- =============================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | =============================================================== -- 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
