Thank you all for your valuable suggestions. I am actually more familiar to
AMBER and do not want to shift to Gromacs for Umbrella Sampling. I was
wondering if there is nice tutorial on Umbrella Sampling via AMBER. That
would be a great help.
Thanks
HM
On Fri, Jan 18, 2013 at 9:21 PM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> 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
> > >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jan 21 2013 - 05:30:02 PST
