Vijayaraj wrote:
My system is a self-assembled cyclic peptide, I am trying to extract PMF
to pull one of the terminal cyclic peptide. I have collected 25 windows
starting from 0.5nm with 0.05nm window size. the histogram shows up to
0.7nm all the windows are overlapped around 0.5nm, and poor sampling
from 0.6 to 0.75nm. from 0.75nm the sampling is perfect. each cyclic
peptide has 8 residues and the terminal one forms 8 hbonds with the 2nd
cyclic peptide. I guess due to this strong hbonding, the sampling window
up to 0.7nm is very poor. If we extend the simulation only for these
windows can we get proper sampling windows? this observation is from
last 10ns of 20ns simulation.
It sounds like you need a substantially stronger force constant to restrain the
positions where the sampling is failing.
-Justin
Message: 3
Date: Mon, 07 Nov 2011 10:20:07 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint"
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4eb7f727.3000...@vt.edu <mailto:4eb7f727.3000...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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>
> <mailto: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> <mailto: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>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> Message-ID:
<20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca
<mailto:20111107090721.jy8zfzhvh4ccw...@webmail.utoronto.ca>
>
<mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
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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