Jianguo Li wrote:
Thanks Justin and Chris and sorry for confusing interpretation.
Let me make it more clear. My peptide is flexible Martini beads, and
highly positively charged. My membrane is a mixture of negatively
charged lipids (25%) and zitterionic lipids(75%). So there is strong
electrostatic attraction
between peptide and membrane. To get the PMF, I did the following:
(1) I did pulling simulation along (0 0 -1) direction to pull my peptide
across the membrane. Then I got different configurations corresponding
to different windows along the reaction coordinates, which is the
z-distance
between peptide and membrane. This figure
(http://www.flickr.com/photos/lijg/5467080971/) shows some of the
configurations at certain reaction coordinates.
Are you not sampling configurations outside of the membrane (i.e. in water)? I
would think that would solve your problem. You don't show any configurations in
which the peptide is completely dissociated from the membrane. I don't know
your objectives, but I would think that if you could completely extract the
peptide from the membrane after passing through it, this would solve your problem.
(2) In each window, I used the corresponding configuration that
generated by the pulling simulation as initial input and run umbrella
sampling. The size of each window is 0.15 nm, but close to the bilayer
cneter (e.g., -0.6<d<0.6), I have
increased number of windows so that the width of the window is to be
0.05 or 0.1 nm, I also tried to use different force constant in these
windows.
From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we
can classify the peptide conformation to be either extended (interacting
with two bilayers) or compact (interacting with only one bilayer).
Ideally, the peptide conformation should be similar for d=x and d=-x.
The problem is that the configuration of peptide is not symmetric with
respect to the bilayer center. For example, the peptide configuration is
compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and
d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the
PMF is not symmetric with respect to the bilayer center. Using more
number of windows and different force constant did not remove the problem.
In my opinion, at least in some windows, the peptide should sample both
compact and extended structure. But what I found is that the windowed
Don't pre-judge the model :) Also, as I said before, there is no reason to
suspect that MARTINI will produce any meaningful secondary structure changes.
It was not parameterized to do so.
umbrella simulation depends on the initial peptide conformation. If the
initial peptide conformation is compact, then after 100 ns, it is still
compact; if the initial peptide in that window is extended, the final
configuration is also extended. I also tried to run longer equilibrium
time (e.g., 200 ns), but the problem still exists.
Sounds like a limitation of the force field model.
My question is how to increase sampling of the peptide conformation? I
just think of two choices:
(1) use high temperature (e.g., 500K) at those bad windows. As I
mentioned, I am wondering if g_wham can unbias the effect of using
different temperatures in different windows.
(2) use REMD in those bad windows. These need a lot of computational
resources.
Neither of these will be useful in generating a sensible PMF curve. WHAM needs
a single temperature for proper weighting. If you start including different
temperatures in different regions of phase space, I would imagine the weighting
would be completely incorrect.
Note that SMD is not the only option for generating starting configurations. If
you think that certain orientations or configurations are "correct," you can
build them yourself, but keep in mind that you'll have to justify this procedure
to a skeptical audience.
-Justin
Is there any other method to deal with the insufficient sampling?
Any suggestions are welcome, thanks for your time reading this email!
Cheers,
Jianguo
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Gromacs Users' List <gmx-users@gromacs.org>
*Sent:* Tuesday, 22 February 2011 11:13:05
*Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
Jianguo Li wrote:
> Thanks for your comments, Justin.
>
> Using timestep of 20 fs, in each window the simulation runs for 100
ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast?
>
Let me clarify things, since I'm not convinced I understand your procedure.
You generate a series of configurations with 0.001 nm/ps pulling, but
then how many windows do you generate for independent simulations? What
are your .mdp parameters during those windows? The pull rate should be
0 during the actual umbrella sampling, to restrain the peptide within
the window. What force constant(s) do you use?
> My system is a little different. My peptide is highly positively
charged. The NMR experiments show that the conformation of the peptide
in water is very dynamic, so I make it flexible without fixing any
secondary structure in Martini model.
As was discussed in the last few days, do not interpret changes in
structure too directly when using MARTINI. It is not designed to
faithfully mimic secondary structure changes.
> In the membrane, 25% of the lipids are negatively charged, so there
are very strong electrostatic attraction between peptides and membrane.
>
> During the peptide approaching the membrane from the top, peptide can
take different configurations at different reaction coordinates. When
pulling the peptide into the membrane, the peptide takes relatively
compact structure and interacts with only the top leaflet until the
distance becomes smaller than 0.45 nm, after that the peptide becomes
extended structure and interacts with both leaflets. This extended
structure remains until the distance becomes -1.05 nm. Further pulling
leads to compact structure and interacts only with the lower leaflet. So
the comformation of the peptide is not symmetric between the center of
the bilayer, which leads to Hysteresis. It seems that there is a huge
I guess I'm confused here, too. The peptide is compact when interacting
with the top leaflet, extended further in the membrane, then compact
again when interacting with the lower leaflet. What's strange about that?
> energy barrier for the peptide to translocate across the membrane
because if the initial conformation in a certain window is extended
(interacting with both leaflets), then it remains extended. Similarly,
it the initial conformation in a certain window is compact (interacting
with only one leaflet), it will remain compact.
>
I don't see how that is necessarily unexpected or problematic. Peptides
will change conformation depending on their environment. If you want a
static structure to cross the membrane (which may or may not represent
reality) you'll have to introduce some kind of intramolecular restraints.
-Justin
> Any Suggestions of dealing with the highly charged system?
>
> Cheers,
> Jianguo
>
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Gromacs Users' List <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> *Sent:* Tuesday, 22 February 2011 09:58:36
> *Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
>
>
>
> Jianguo Li wrote:
> > Thanks Justin.
> > I tried your suggestions by either increase more windows and
change the force constant, but it seems the samplings are still bad in
some windows. When I did pulling in (0 0 1) direction and a reverse
pulling in (0 0 -1) direction, I got different configurations at certain
reaction coordinates. And the windowed umbrella sampling seems depends
strongly on the initial configurations in that window. Therefore I got
different PMFs using pulling in (0 0 1) direction and reverse pulling in
(0 0 -1) direction.
> >
>
> How long are each of the simulations in each window? Sufficient
sampling should eliminate any configurational bias and/or hysteresis.
Also, if the pulling that sets up the initial configurations is done
slowly enough, you won't see these problems. Sounds to me like you're
pulling too fast or hard, such that the system is not stable.
>
> > In my simulation, I exert constraints on phosphate atoms in z
direction, so there is no lipid flip-flop and the membrane will be
stable at high temperatures. Then I am thinking of increasing
temperature in those bad windows to enhance sampling...
> >
>
> I don't know if I can make a convincing argument here, but
intuitively, these windows would be sampling in a different ensemble, so
the free energy landscape in these windows would be discontinuous with
any adjacent windows that are done at different temperatures, and
perhaps the forces required to restrain your peptide at a given COM
distance will still result in a discontinuous PMF. I would also suspect
that g_wham can't handle this situation; it has a -temp flag, but it
only takes one value. So if you construct your PMF curve using WHAM,
but supply incorrect or inconsistent information, I certainly wouldn't
believe the result.
>
> I guess the main point is, there are tons of published demonstrations
of peptides and other molecules crossing a membrane with SMD and
umbrella sampling, so it should be possible to generate stable
configurations without any funny tricks.
>
> -Justin
>
> > best regards,
> > Jianguo
> >
> >
> >
> >
------------------------------------------------------------------------
> > *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
> > *Sent:* Tuesday, 22 February 2011 09:35:37
> > *Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
> >
> >
> >
> > Jianguo Li wrote:
> > > Dear all,
> > >
> > > I want to get the PMF of my peptide across the membrane
bilayer. First I pulled my peptide across the membrane and then did
windowed umbrella sampling along the reaction coordinates which is the
z-distance between peptide and membrane. However, I found that sampling
is not sufficient in some windows(e.g., around the center of the
membrane). To enhance the sampling, I am thinking to run the simulation
in those windows at higher temperature (e.g., 500K), but this will
introduce a bias. My question is: can g_wham remove the bias due to
using different temperatures in different windows?
> > >
> > > If g_wham cannot deal with the bias due to using different T, I
may need to do REMD in those windows. But that will be very expensive
computationally. Anybody have an idea of enhancing sampling in those
windows?
> > >
> > > Btw, I am using Martini CG model.
> > >
> > > Any suggestions will be highly appreciated, thank you!
> > >
> >
> > A more straightforward approach is to (1) add more sampling
windows or (2) increase the force constant in regions where there's poor
sampling, or perhaps both.
> >
> > -Justin
> >
> > > Cheers,
> > > Jianguo
> > >
> >
> > -- ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users@gromacs.org
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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