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 Mon Jan 21 2013 - 16:00:02 PST
