Re: [gmx-users] How to use Inflategro with different lipid types
Ioannis Beis wrote: Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distance of center of mass of neighboring lipids is 1 nm, so there are small areas with overlaps. I was hoping that I would be able to inflate my membrane and have the lipids totally free of overlaps using Inflategro. Subsequently, I was planning to use the shrinking steps to bring the membrane into physiological size. Is this strategy valid in the first place? If not, I kindly ask for an alternative. In case this method can be used, despite To identify the lipid species their actual residue name must be given which is mentioned in the methodology, the form INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein) only allows the use of one lipid type. How is it possible to run perl with all lipid types at once? I have tried performing inflations using one lipid type at a time and they work. [It worths mentioning that the coordinates of the rest two (uninflated) lipid types slightly change without equilibration (I assume this has to do with Inflategro trying to force the molecules avoid overlaps)]. But I can't treat my membrane as a system that way. I have read the publication introducing the methodology, but it didn't help me solve my problem. I would be grateful if someone could help, also taking into account that I am inexperienced. If you want to use InflateGRO, then you'll have to modify the code to do so. It handles only one lipid type. The alternative is to use normal MD simulations to pack the membrane. On such approach (just thinking out loud here, so it may not work) might be to simulate your membrane (maybe without water) with some external pressure applied to the x-y plane to compress the lipids together. You may need position restraints on, i.e., the lipid headgroups in the z-dimension only during this procedure so the lipids do not simply slam into one another and distort the membrane. Once you've achieved a reasonable membrane, solvate and equilibrate for a longer period of time in the presence of solvent and absence of any restraints. -Justin Kindest regards, Yiannis -- 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] How to use Inflategro with different lipid types
Hi, To construct the bilayer I would just take an equilibrated POPC bilayer and then randomly pick lipids to change to POPE (just by a simple renaming of these lipids and the atom names in the headgroup) and DPPC (which would just require deletion of two united-atoms from the sn-2 chains and renaming of the lipids). Then just run for an equilibration on the bilayer to allow the changes to take effect. There are other approaches you could take but I see this as the simplest solution. Cheers Tom Justin A. Lemkul wrote: Ioannis Beis wrote: Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distance of center of mass of neighboring lipids is 1 nm, so there are small areas with overlaps. I was hoping that I would be able to inflate my membrane and have the lipids totally free of overlaps using Inflategro. Subsequently, I was planning to use the shrinking steps to bring the membrane into physiological size. Is this strategy valid in the first place? If not, I kindly ask for an alternative. In case this method can be used, despite To identify the lipid species their actual residue name must be given which is mentioned in the methodology, the form INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein) only allows the use of one lipid type. How is it possible to run perl with all lipid types at once? I have tried performing inflations using one lipid type at a time and they work. [It worths mentioning that the coordinates of the rest two (uninflated) lipid types slightly change without equilibration (I assume this has to do with Inflategro trying to force the molecules avoid overlaps)]. But I can't treat my membrane as a system that way. I have read the publication introducing the methodology, but it didn't help me solve my problem. I would be grateful if someone could help, also taking into account that I am inexperienced. If you want to use InflateGRO, then you'll have to modify the code to do so. It handles only one lipid type. The alternative is to use normal MD simulations to pack the membrane. On such approach (just thinking out loud here, so it may not work) might be to simulate your membrane (maybe without water) with some external pressure applied to the x-y plane to compress the lipids together. You may need position restraints on, i.e., the lipid headgroups in the z-dimension only during this procedure so the lipids do not simply slam into one another and distort the membrane. Once you've achieved a reasonable membrane, solvate and equilibrate for a longer period of time in the presence of solvent and absence of any restraints. -Justin Kindest regards, Yiannis -- Dr Thomas Piggot University of Southampton, UK. -- 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] How to use Inflategro with different lipid types
Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distance of center of mass of neighboring lipids is 1 nm, so there are small areas with overlaps. I was hoping that I would be able to inflate my membrane and have the lipids totally free of overlaps using Inflategro. Subsequently, I was planning to use the shrinking steps to bring the membrane into physiological size. Is this strategy valid in the first place? If not, I kindly ask for an alternative. In case this method can be used, despite To identify the lipid species their actual residue name must be given which is mentioned in the methodology, the form INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein) only allows the use of one lipid type. How is it possible to run perl with all lipid types at once? I have tried performing inflations using one lipid type at a time and they work. [It worths mentioning that the coordinates of the rest two (uninflated) lipid types slightly change without equilibration (I assume this has to do with Inflategro trying to force the molecules avoid overlaps)]. But I can't treat my membrane as a system that way. I have read the publication introducing the methodology, but it didn't help me solve my problem. I would be grateful if someone could help, also taking into account that I am inexperienced. Kindest regards, Yiannis -- 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
