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

[NG HUI WEN]

Thanks Justin. I got it now.


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Wednesday, October 13, 2010 12:07 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Equilibration of POPC - Lipid molecules jump
outof box



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>
> 
>  >>
> 

-- 
========================================

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

========================================
-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
<< Email has been scanned for viruses by UNMC email management service
>>
<< Email has been scanned for viruses by UNMC email management service >>