Re: [gmx-users] comm-grps for a membrane-protein-ligand system
Peter C. Lai wrote: 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 There is no "center" to a periodic system. Molecules diffuse, there's no way around it. If you try to apply some biasing force to fit some visualization convenience, you're potentially damaging the simulation's integrity. 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 10 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 1 kJ/mol during NPT equilibration). Position restraints do not fix anything in place, they merely provide an energy barrier that penalizes change. If your goal is simply to obtain a reasonably equilibrated system, then there is no need for a force constant above about 1000, otherwise you may be overtly influencing the ability of your system to respond to change. -Justin 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] comm-grps for a membrane-protein-ligand system
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 10 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 1 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 listgmx-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 listgmx-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
Re: [gmx-users] comm-grps for a membrane-protein-ligand system
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 listgmx-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
[gmx-users] comm-grps for a membrane-protein-ligand system
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... -- === 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 listgmx-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
