[gmx-users] Equilibration of POPC - Lipid molecules jump outof box
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Wed Oct 13 08:19:53 CEST 2010
Thanks Justin. I got it now.
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
NG HUI WEN wrote:
> Dear gmxusers,
> I have obtained a box of POPC with a starting dimension of 12.48,
> 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
> homogenous before I embed a protein into the bilayer.
> What I did was :-
> 1) Energy minimize the new bilayer with the steepest descent
> - converged at 131^st step (final potential energy= -8.8059400 e+05)
> 2) Perform a brief 100ps NVT on the bilayer with position
> on the phosphate atom (fc= 1000 on the z axis only). The water layer
> found to be non-homogenous after this step.
> 3) Perform NPT (still with position restraint on P atom). The
> layer became more and more homogenous as I extended the NPT
> equilibration step. However, I now have a new problem. After 6ns of
> 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.
> Many thanks for you help.
> Email has been scanned for viruses by UNMC email management service
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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