Hi All,
For all those that were interested in an Umbrella sampling tutorial I have
put it up on the tutorial website
http://ambermd.org/tutorials/ as
Tutorial A17. It should be up public on the site within a day or so.
All the best
Ross
On 1/22/13 12:35 AM, "HM" <scienceamber.gmail.com> wrote:
>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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Received on Sun Jan 27 2013 - 17:00:02 PST
