shahid nayeem wrote:
Thanks Justin. I will try again. But please refer to some protocol if
you know and one last question that before doing umbrella sampling
simulation how can one be sure that the pulling is good and one should
go ahead with selecting window and doing umbrella sampling. In the end
when you see histo.xvg and profile.xvg , it cost a lot computationally
and if you don't get it right these computational resources are wasted.
There are certainly simulations that have been published using umbrella sampling
on a variety of systems. I'm sure some relatively quick literature searching
will lead you to some suitable ideas. Spending a few hours doing some reading
will save you months of wasted CPU time.
-Justin
Shahid nayeem
On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shahid nayeem wrote:
Thanks for quick reply. I have created mutant of a complex by
changing interface residue in VMD. These mutant are
experimentally known to show less binding affinity. I want to
reproduce these results with umbrella sampling. Now I am sending
profile and histo file for wt and mutant. Please suggest where i
am wrong.
The PMF curves look poorly converged. Your reaction coordinates are
not the same for both the WT and mutant (you appear to have a far
shorter reaction coordinate for the mutant). The energy minimum is
also ill-defined for the mutant.
As for the reason behind these phenomena, I cannot say, nor do I
have time to sort through your data and try to work it out for you.
Refer to the literature, find similar protocols, and proceed from
there.
-Justin
Shahid Nayeem
On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
shahid nayeem wrote:
Dear Justin
I am doing umbrella pulling simulation of a protein
complex wt
and mutant. I expect mutant to give lower deltG value. I am
attaching a tif file of energy vs time curve of wt and mutant
protein on pulling simulation. These energies are obtained by
g_energy and selecting 11 option which is COM pulling
energy. In
this curve the first peak decreases and again rises at longer
time. How many windows should be selected. As expected
the peak
of COM pulling energy is lower in mutants. Please explain why
the energy again rises at higher time. Should I use the
windows
upto 160ps only because thereafter in both curve there is
rise
in energy value. the pull code used is as follows.
What you have obtained is a path-dependent energy that may or may
not signify anything useful - it almost certainly does not. I
cannot offer an explanation of the sharp increase towards the
end of
the simulation other than to speculate that your box is of
insufficient size and you're encountering PBC issues.
As for how many windows are necessary, it's also impossible
to tell.
You need enough windows to adequately sample the reaction
coordinate. Thus, it is decided based on how far you need to
separate the two species, how strong the force constant is during
the US simulations, the nature of the interactions in the
system and
how fast they converge, etc.
-Justin
pull_geometry = distance pull_dim = Y N Y
pull_vec1 = 0.75 0 1
pull_start = yes pull_ngroups = 1
pull_group0 = Chain_B pull_group1 = Chain_A
pull_rate1 = 0.01 pull_k1 = 1000
-- ==============================____==========
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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
==============================____==========
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>
Please search the archive at
http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<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>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read
http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<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
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<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
<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
