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>
*To:* Discussion list for GROMACS users <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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
