[gmx-users] Equilibration of POPC - Lipid molecules jump out of box

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Tue Oct 12 16:09:45 CEST 2010

Dear gmxusers,


I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and 6.92 (nm) using genconf -nbox 2  2  1. The original lipid was downloaded from Prof. Tieleman's site (popc128a.pdb).


My intention is to equilibrate the new bilayer such that the lipids, particularly at the borders where replication occurred, are sufficiently homogenous before I  embed a protein into the bilayer. 


 What I did was :-

1)      Energy minimize the new bilayer with the steepest descent method - converged at  131st step (final potential energy= -8.8059400 e+05)

2)      Perform a brief 100ps NVT on the bilayer with position restraint on the phosphate atom (fc= 1000 on the z axis only). The water layer was found to be non-homogenous after this step.

3)      Perform NPT (still with position restraint on P atom). The water layer became more and more homogenous as I extended the NPT equilibration step. However, I now have a new problem. After 6ns of NPT, I viewed my lipids with VMD and noticed that a few lipid molecules appeared outside the box. I then extended the simulation for another 6 ns and the problem still persists. 


I am confused why this phenomena occurred, especially when there was a position restraint on the P atom.


Many thanks for you help.



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