HM,
You placed the peptide next to the lipid bilayer with VMD. It sounds like you expect the peptide insert into the membrane and cross the bilayer, but it diffused away. If you're simply trying to observe the peptide interacting with or crossing the bilayer, you'll probably need a large amount of sampling in hopes of seeing a peptide-bilayer interaction. With periodic boundaries, the peptide will (eventually) interact with the bilayer.
But the questions are: Why is this a control? What are you measuring or investigating in this study? Is this really an appropriate method/approach? It's not clear what your methodology is.
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: HM [scienceamber.gmail.com]
Sent: Thursday, January 17, 2013 2:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane)
Dear Ben,
Thank you for your reply. Here I am giving detail of my system:
Peptide: 10 amino acid long ( known to interact and penetrate across the
membrane)
Lipid molecules: 274 (bilayer)
lipid type: POPC, forcefield : gaff
AMBER version: Amber10 sander
Behaviour expectation: I expect during my simulation the peptide should
cross the membrane
Thanks and Regards,
HM
On Tue, Jan 15, 2013 at 6:49 PM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> HM,
>
> It's not clear what your approach is for this simulation. How exactly is
> your system set up (i.e. system size, number of lipid bilayers, number of
> waters, number of peptides)? What is the peptide and the mechanism of
> transport across the membrane? Can you clarify what behavior you expected
> from this simulation?
>
> In addition, there's already been some work done in our group and our
> collaborators for lipid parameter sets for Amber. Take a look at the
> parameter sets Lipid11 and GAFFlipid (Skjevik et al, J. Phys. Chem. B,
> 2012; Dickson et al, Soft Matter, 2012).
>
> Ben Madej
> Walker Molecular Dynamics Lab
>
> On Jan 15, 2013, at 9:18 AM, HM <scienceamber.gmail.com> wrote:
>
> > Hi All,
> > In my study, I am trying to see the membrane penetrating behavior of few
> > peptides. As a control, I took the peptide which is well known to cross
> the
> > membrane. I prepared the peptide structure (20 amino acid long ) and 20
> ns
> > simulation to get the stable conformation. Now I prepared the membrane
> > (POPC) and kept the peptide over the membrane (using VMD). I generated
> the
> > lipid parameters using AM1-BCC method and then performed the simulation
> > (minimization, heating, equilibration.)
> >
> > Now during simulation the peptide goes away ( within ns) from the lipid
> > membrane and it never comes back ( during simulation of 20ns).
> >
> > I guess there is no point of continuing the simulation ? Can you please
> > help me to get rid of this issue.
> >
> > Thanks,
> > HM
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> > AMBER.ambermd.org
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>
>
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