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 equilibration. To solve the problem, I was trying to turn off the bond constraints, i.e. constraints = none, and restart 2-ns equilibration. It seemed that everything is OK after the new equilibration (no bond was broken and the protein backbone changed structurally slightly). Next I continued 1-ns equilibration adding the bond constraints again and no LINCS warning happened. Before conducting my production MD with the files from the above procedure, I am eager to clarify some confusion for my simulation, that is: 1. Whether my operations (especially turning off the bond constraints during equilibration) are accepted theoretically for a good MD simulation? 2. If not, should I repeat energy minimization for the system? Be honest, emtol = 500 is where the system can reach until now with my best try. Maybe I have ignored other applicable EM or equilibration operations besides the GMX manual? 3. If yes, what should I do to guarantee the correct foundation of the current membrane-protein structure, like checking the bond change, or any other means? Thanks for considering my problems. Best wishes, Darcy
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