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

[Justin A. Lemkul]

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  
> 
> <<
> 
> Email has been scanned for viruses by UNMC email management service 
> <http://www.nottingham.edu.my>
> 
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> 

-- 
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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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