From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Mar 28 2011 - 09:06:40 CDT
> Dear Jerome,
>
Thank you for the comforting thought about umbrella sampling:)
>
My system is an alpha helix made of 35 alanines, spin labelled in the middle
(position 18) and put in a DMPC membrane. The spin label is a bulky
side-chain, comparable to trypthopan in size. The reaction coordinates are
the theta and phi angles of the vector from the labels Ca atom to the last O
atom.
> At first I wanted to spin label different positions on the peptide, but
right now I don't think this is the best idea. If I run several 2D free
energy scans at different positions, I will not get the offset between them
(as each scan will have the zero set to it's global minimum). But If I
define the membrane depth as another colvar and run what is effectively a 3D
scan then the offsets between various 2D scans will be correct. The depth
colvar would be the distance between the COM of the membrane and the C-alpha
of the spin label.
A simple 1D depth scan will probably not help either, because the other
degrees of freedom (the thetha and phi colvars) are to slow. Is my reasoning
sound? I think I have just enough computer power to perhaps converge a 3D
ABF free energy scan.
>
two further questions:
>
- What did you mean by monitoring relaxation? (currently I just watch
each ns how the PMF converges).
- If I set a distanceZ colvar between (0, 0,0) and the COM of the
membrane (using the phosphate heads), will this be handled correctly if half
of the membrane passes into the "next" periodic cell? I think I should use
*forceNoPBC *but I'm not sure how the coordinates are stored internally.
I would like to move the COM of the membrane from the middle of the unit
cell to the top.
Thank you for your help & best regards,
> Ajasja
>
On Fri, Mar 25, 2011 at 12:25, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>
Hi Ajasja,
>
>>
> It's hard to have a gut feeling when you didn't tell us anything about
>
>> your system. As a comparison though, remember that people who do
>
>> umbrella sampling would probably chop up this space into at least a
>
>> hundred windows, and suffer any convergence problems that would arise.
>
>> The difference is, they would have no other choice (besides
>
>> relinquishing umbrella sampling entirely). So whatever you end up
>
>> doing, you can find comfort in the fact that it's better than umbrella
>
>> sampling.
>
>>
> Anyway, the questions are: are there degrees of freedom other than
>
>> your RCs that can get stuck? (hint: the answer is yes) and then: how
>
>> much do the RCs have to move about to give those a chance to get
>
>> unstuck (and how long will it take)? That should give you an idea of a
>
>> minimum size for the quadrants, and a minimum sampling time for each
>
>> of them (of course that can and should be adjusted by monitoring
>
>> relaxation in the simulations).
>
>>
> Cheers,
>
>> Jerome
>
>>
> On 25 March 2011 10:52, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> wrote:
>
>> > Dear all,
>
>> > Is there any advisable limit on how many quadrants a 2D torsional free
>
>> > energy scan using ABF can be divided? Scaling the simulation by
> splitting
>
>> > the ABF calculation has the advantage that each part runs independently,
> so
>
>> > there are no scaling issues.
>
>> > On the other hand one is wary of introducing artifacts by the artificial
>
>> > wall constraints (as in figure 6b in [1]).
>
>> > I'm asking because over the weekend I will have access to 512 cores. My
>
>> > simulation has 16.000 atoms, so just throwing more cores at it will not
> be
>
>> > very effective. (I will of course run the necessary scaling benchmarks
>
>> > before I start)
>
>> > Currently I'm spliting the ABF calculation into 8 parts. Would 36 parts
> be
>
>> > too much? This would then be pieces of 6x6 points.(The bin width is 10
>
>> > degrees and the range form -180 to 180).
>
>> > I know this strongly depends on the system, but I'm asking for the "gut"
>
>> > feeling:)
>
>> > Thank you & best regards,
>
>> > Ajasja Ljubetič,
>
>> > Young reasercher,
>
>> > Laboratory of biophysics,
>
>> > Institute Jožef Štefan,
>
>> > Ljubljana, Slovenia
>
>> >
>
>> > Christophe Chipot and Jérome Hénin, “Exploring the free-energy
> landscape
>
>> > of a short peptide using an average force,” The Journal of Chemical
> Physics
> > 123, no. 24 (2005): 244906.
>
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