There's been some good suggestions about how you might proceed with your peptide-bilayer system.
In order to differentiate peptide-crossing behavior, Ross's suggestion to use an umbrella sampling method to generate a potential of mean force (PMF) would be one approach.
I would also strongly recommend that you still use an explicit solvent for the lipid simulations. As Thomas mentioned, the attempts to use an implicit solvent have had additional issues. It's already non-trivial to simulate a bilayer properly with explicit solvent.
All the best,
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: Thomas Evangelidis [tevang3.gmail.com]
Sent: Friday, January 18, 2013 7:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane)
Simulating protein-membrane systems in implicit solvent is a complicated
task and I don't think there are thoroughly tested protocols to do that in
AMBER or any other popular MD engine. I know CHARMM supports implicit
solvent - implicit membrane simulations, although with some known
inaccuracies.
Thomas
On 18 January 2013 11:07, HM <scienceamber.gmail.com> wrote:
> Thank Ross,
> I am new to Umbrella Sampling, It would be nice if I will get some help
> from a nice tutorial. I searched but could not find a good one.
> I have a query regarding the system complexity. Since I have limited
> processors to run the job, shall I try Umbrella Sampling in implicit
> solvent, will the results reliable?
>
> Thanks,
>
> On Fri, Jan 18, 2013 at 9:38 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > would take a good look in the literature at what people do in these
> > situations. The issue with your 'control' is that you make no mention of
> > timescale. The experimental data may indeed show that the peptide
> > penetrates the membrane but does it give any indication of the timescale
> > that this takes? If it is on the order of milliseconds then just running
> > brute force MD is not going to work. One option would be to try some form
> > of umbrella
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 18 2013 - 12:30:03 PST
