I'm not sure I follow your discussion about a dry interface. If you got
shake failures in a "normal" simulation, then something else might be
wrong. I don't really ever get them unless i have a bad structure, or bad
force field parameters. Normal MD should be fine for simulations using our
standard force field libraries.
carlos
On Fri, Feb 17, 2023 at 1:08 PM He, Amy <he.1768.buckeyemail.osu.edu> wrote:
> Hi Dr. Simmerling,
>
>
>
> Thanks for your kind response.
>
>
>
> I was thinking about doing this because from some SHAKE failures I
> previously got, my feeling is that a dry interface can be rough for a shake
> atom and unshaken atom. (I think there’s a chance that LJ potential can
> blow up, but maybe because my choice/reference structure is just bad and
> there are other underlying reasons..
>
>
>
> Such direct/dry interface can always exist unless we unshake the entire
> solute, which is what I did to resolve the issue. For waters --
>
>
>
> If waters are present at these “rough” interface, then the translational
> motion of waters can do some “buffering” effect to the shake/unshake,
> chemical/alchemical interface a little bit. But if we need to look at the
> energetics, would possibly it be better to also unconstrain these waters?
>
>
>
> You are right that waters are commonly set to be rigid. Also the mask
> specification could be hard since they could be interchangeable. Maybe that
> is possible if a distance-based selection is made, but the number of
> unshaken waters might also need to be constant (since the constraints
> should be considered part of the potential energy function)..
>
>
>
> We are not planning to implement conditional constraints on solvents
> without further validation. But I am curious if there’s already some tested
> options/if anyone might have the same interest into doing that.
>
>
>
> Thanks again for your time and kind advice, as always.
>
>
>
>
>
> Many Thanks,
>
> Amy
>
>
>
> *From: *Carlos Simmerling via AMBER <amber.ambermd.org>
> *Date: *Friday, February 17, 2023 at 12:52 PM
> *To: *He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <
> amber.ambermd.org>
> *Subject: *Re: [AMBER] Method (SHAKE/SETTLE, HMR) to conditionally
> constrain waters
>
>
>
> Are you saying that you want to not use shake on some of the water? The
> coomon water models are intended to be rigid, so you would need a good
> reason for this, and understand that the models may not perform well. Also
> they are likely to diffuse and it would be hard to turn on/off dynamically
> (unless they are very buried).
>
> On Fri, Feb 17, 2023, 12:37 PM He, Amy via AMBER <amber.ambermd.org>
> wrote:
>
> > Dear Amber Community,
> >
> > I’m using sander in Amber20 for MD simulations. I just have a very very
> > quick question about options to constrain explicit waters:
> >
> > With ntc = 2, SHAKE is applied to solutes and SETTLE for waters. Using
> > option “no_shake” along with ntf = 1, we can conditionally SHAKE (or
> > unshake) part of the system. So..
> >
> > Is there possibly a way to conditionally unshake, or repartition the mass
> > of the waters in a distance-specified region?
> >
> > If I do a “conditional” SHAKE, am I essentially modifying the potential
> > energy function of my system? Is the error (difference with respect to
> > choices of unshaken atoms) estimatable?
> >
> >
> > Bests,
> > Amy
> >
> >
> > --
> > Amy He
> > Chemistry Graduate Teaching Assistant
> > Hadad Research Group
> > Ohio State University
> > he.1768.osu.edu<mailto:he.1768.osu.edu <he.1768.osu.edu>>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!1aycPGia9Kqz0VrIEVlLX1xTDvb7Wrq12wGrDtRgS34yCMQ89YF_1KHd3BmXJ_aQ5IEZrmo_XZPUwnWsB8fzzCJMys4$
> <https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!1aycPGia9Kqz0VrIEVlLX1xTDvb7Wrq12wGrDtRgS34yCMQ89YF_1KHd3BmXJ_aQ5IEZrmo_XZPUwnWsB8fzzCJMys4$>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!1aycPGia9Kqz0VrIEVlLX1xTDvb7Wrq12wGrDtRgS34yCMQ89YF_1KHd3BmXJ_aQ5IEZrmo_XZPUwnWsB8fzzCJMys4$
> <https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!1aycPGia9Kqz0VrIEVlLX1xTDvb7Wrq12wGrDtRgS34yCMQ89YF_1KHd3BmXJ_aQ5IEZrmo_XZPUwnWsB8fzzCJMys4$>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 17 2023 - 13:30:02 PST
