do you mean multi-dimensional umbrella sampling? yes it is possible, though
more complex and expensive.
there are many papers on this, but some examples from my group include:
Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations
Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric
Pocket. Lucy Fallon, Kellon A. A. Belfon, Lauren Raguette, Yuzhang Wang,
Darya Stepanenko, Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah
Varghese, Christopher P. Corbo, Robert C. Rizzo, and Carlos Simmerling, J.
Am. Chem. Soc., 2021, 143, 30, 11349–11360. doi.org/10.1021/jacs.1c00556
Rational modulation of the induced-fit conformational change for slow-onset
inhibition in M. tuberculosis InhA. Lai, C-T., Li, H; Yu, W., Shah, S.,
Bommineni, G., Perrone, V., Garcia-Diaz, M., Tonge, P., Simmerling, C.,
Biochemistry, 2015, 54 (30), 4683-4691
Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase.
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C., Journal of the American Chemical Society, 2011, 133, 14504–14506
On Fri, Sep 15, 2023 at 1:59 PM Jing Qu via AMBER <amber.ambermd.org> wrote:
> Hi,
>
> If I need to change two reaction coordinates simultaneously(or even more),
> how should I do or where should I start? Is there any instructions to do
> so? Thanks!
>
> Best,
> Jing
>
> Jing Qu <jqu2.ncsu.edu>于2023年9月8日 周五19:19写道：
>
> > Yes it's more like that. Thank you. I'll have a look at it and have a
> try.
> >
> > Carlos Simmerling <carlos.simmerling.gmail.com>于2023年9月8日 周五18:09写道：
> >
> >> Do you mean the base rotates out of the duplex? In that case maybe look
> >> at this article
> >>
> >> An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
> >> https://doi.org/10.1021/ct9001575
> >>
> >>
> >> On Fri, Sep 8, 2023, 5:15 PM Jing Qu <jqu2.ncsu.edu> wrote:
> >>
> >>> Hi,
> >>>
> >>> If you're referring to variations of chi torsion angles then that's not
> >>> what I'm trying to say here. I mean that the bases rotate around the
> z-axis
> >>> (which is the normal vector to the base plane) with the C1' atom as the
> >>> origin. Or with the other end of the glycosidic bond as the origin. Or
> >>> maybe even rotating the base and the sugar ring together as a whole.
> >>>
> >>> Best,
> >>> Jing
> >>>
> >>> On Fri, Sep 8, 2023 at 4:58 PM Carlos Simmerling <
> >>> carlos.simmerling.gmail.com> wrote:
> >>>
> >>>> If you mean rotation of the base around the glycosidic angle, you can
> >>>> use a dihedral restraint.
> >>>> This old reference might help
> >>>> https://doi.org/10.1021/ja075128w
> >>>>
> >>>> On Fri, Sep 8, 2023, 4:52 PM Jing Qu via AMBER <amber.ambermd.org>
> >>>> wrote:
> >>>>
> >>>>> Dear all,
> >>>>>
> >>>>> I am learning to perform the Umbrella Sampling to get the PMF between
> >>>>> two
> >>>>> states of a DNA strand. And I have trouble determining the reaction
> >>>>> coordinates. The difference between the two states is that the
> hydrogen
> >>>>> bonds they form are not the same. I think the transition is more like
> >>>>> rotating the base in the plane of the base ring (around the z-axis).
> I
> >>>>> see
> >>>>> that the tutorial examples on Amber's site use reaction coordinates
> >>>>> like
> >>>>> angles or distances. But I can't think of any angle that would
> control
> >>>>> the
> >>>>> transition of the structures I have. Anyone have suggestions?
> >>>>>
> >>>>> Thanks in advance,
> >>>>> Jing
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
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Received on Fri Sep 15 2023 - 11:30:03 PDT
