[gmx-users] Number of windows in umbrella sampling
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 14 15:02:29 CET 2012
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>>
>
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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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <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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