Vijayaraj wrote:
and also I tried to plot the PMF curve from this data, I got few warning
messages like "no data point in bin 20, You may not get a reasonable
profile. Check your histograms!". the histogram shows poor sampling from
0.6 nm to 0.7 nm, and the windows in this position completely overlaps
at 0.5-0.6 nm. should we have to extend the simulation for 0.6-0.7 nm
window to get the restrain distance converged?
It is still somewhat difficult to provide any useful advice. You haven't stated
what your system is, how your windows were assembled, at what interval they
exist, or how many you have. The above warnings suggest that you've either set
up the windows wrong, have insufficient data, or are analyzing parts of the
trajectory you shouldn't be (i.e. initial times that are equilibration).
-Justin
On Mon, Nov 7, 2011 at 3:53 PM, Vijayaraj <vijayara...@gmail.com
<mailto:vijayara...@gmail.com>> wrote:
Hello,
Thanks for the suggestions. I did umbrella simulation for 20ns and
the pull force is as below.
19960.0000 -6.78192
19962.0000 33.3579
19964.0000 -3.1808
19966.0000 -15.0304
19968.0000 -55.4436
19970.0000 -38.9422
19972.0000 -9.41927
19974.0000 -5.95981
19976.0000 0.626319
19978.0000 2.28736
19980.0000 23.5115
19982.0000 10.6415
19984.0000 -0.233446
19986.0000 8.26525
19988.0000 36.7656
19990.0000 26.6017
19992.0000 64.43
19994.0000 53.3844
19996.0000 18.3834
19998.0000 39.8988
20000.0000 43.6291
I expect the force should be converged. my understanding might be
wrong. I have poor knowledge about this umbrella sampling
convergence and image selection for the PMF calculation. is this
fluctuation in force due to pulling group motion out of box? can you
give me some idea about the selection of images for PMF calculation?
I found from the pullx files that the COM distance converges after
few ns of simulation. I understood that we cant do PMF study with
pull=constraint.
Vijay.
Message: 2
Date: Mon, 07 Nov 2011 09:07:21 -0500
From: chris.ne...@utoronto.ca <mailto:chris.ne...@utoronto.ca>
Subject: [gmx-users] umbrella sampling with "pull=constraint"
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID: <20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca
<mailto:20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca>>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear Vijay:
Can you please provide evidence for your claim that the harmonic
potential is not applied properly, since you may decide to use
pull=umbrella once you have set that up correctly. Importantly,
movement out of the unit-cell is not a problem, as discussed a
lot on
this list. Nevertheless, you do need to worry about which images are
used to derive the pulling forces. You can often do that by a
judicious selection of pull_pbcatom (read about that on-list and in
the manual). In some cases, however, pull_pbcatom can not assist
enough and you are forced to make the box larger. None of this is
alleviated by pull=constraint, which is why I'm not going to answer
your question about your .mdp parameters at this point. Let's
get the
problems identified and solved first with pull=umbrella.
Chris.
-- original message --
Hello,
I have done umbrella sampling with "pull=umbrella" and I found
that the
pulling group has high fluctuations and sometimes moving out of the
periodic box. I think that the harmonic potential is not
properly applied
and thus the pulling group is not retained with the specified
COM distance
between the reference and pulling group. Can we use
pull=constraint option
to retain the pulling group within the COM distance? my pulling
code is as
bellow with restrain at 0.5nm distance from ref group. I just
want to get
some idea about this pull code modification.
pull = constraint
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_ngroups = 1
pull_group0 = Chain_A
pull_group1 = Chain_B
pull_init1 = 0.50
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 500
pull_nstfout = 500
Regards,
Vijay.
-
--
========================================
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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