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>
*To:* Gromacs Users' List <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>>
> *To:* Discussion list for GROMACS users <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
========================================
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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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