[gmx-users] Bond constraints during the equilibration for membrane-protein system

Dear All I am conducting a MD simulation for membrane protein with GMX 4.0.5. I met lots of LINCS warnings (almost for angle change of N-H and C-H bond) when doing equilibration for the membrane-protein system under NPT condition. I had doing energy minimization (emtol = 500) before the equilibr

Re: [gmx-users] Bond constraints during the equilibration for membrane-protein system

li lv wrote: Dear All I am conducting a MD simulation for membrane protein with GMX 4.0.5. I met lots of LINCS warnings (almost for angle change of N-H and C-H bond) when doing equilibration for the membrane-protein system under NPT condition. I had doing energy minimization (emtol = 500

Re: [gmx-users] Bond constraints during the equilibration for membrane-protein system

Dear Justin Thanks for your reply. Generally I conduct the simulation following the tutorial on your website. The system contains an integrin alpha2b/beta3 transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and solvated in water. The initial membrane-protein system is built

Re: [gmx-users] Bond constraints during the equilibration for membrane-protein system

li lv wrote: Dear Justin Thanks for your reply. Generally I conduct the simulation following the tutorial on your website. The system contains an integrin alpha2b/beta3 transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and solvated in water. The initial membrane-pro

Re: [gmx-users] Bond constraints during the equilibration for membrane-protein system

Dear Justin Thanks greatly for your suggestions. I will try a new series of EMs and NPT equilibrations to find whether it will be of effect. Li 2011/5/14 Justin A. Lemkul > > > li lv wrote: > >> Dear Justin >> >> >> Thanks for your reply. Generally I conduct the simulation following the >> tu