[gmx-users] Number of windows in umbrella sampling
msnayeem at gmail.com
Tue Feb 14 05:01:42 CET 2012
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.
On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul <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.
> Shahid Nayeem
>> On Mon, Feb 13, 2012 at 7:15 PM, Justin A. Lemkul <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.
>> 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> | (540) 231-9080
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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
> gmx-users mailing list gmx-users at gromacs.org
> 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
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