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

[li lv]

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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