[gmx-users] Number of windows in umbrella sampling
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 13 15:42:51 CET 2012
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
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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