Hi Ross,
That would help a lot. :-)
Thanks,
Hirdesh
On Tue, Jan 22, 2013 at 12:47 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi HM
>
> I have an umbrella sampling tutorial - just haven't had a chance to put it
> up on the webpage yet. I'll send you a copy off list to try.
>
> All the best
> Ross
>
>
>
>
>
> On 1/21/13 5:25 AM, "HM" <scienceamber.gmail.com> wrote:
>
> >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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> >> >
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Received on Tue Jan 22 2013 - 01:00:02 PST
