NG HUI WEN wrote:
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 131^st 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.
Please see FAQ #11.
http://www.gromacs.org/Documentation/FAQs
-Justin
Many thanks for you help.
HW
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--
========================================
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
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