The traditional force switch definition includes a potential shift - you
can't long-range correct a potential that is rigorously short range. You
can define the shift differently, such that a correction is well defined,
but then there is an energy discontinuity (but no force discontinuity) at
the cutoff.
If you look at all of the popular methods, a cutoff around 9/10 A seems to
pretty much hide all of the issues that each has, at least within numerical
precision. It's also becoming fashionable to do full long-range evaluations
of Lennard-Jones using PME, which solves all of the above issues.
HTH,
BKR
On Fri, Dec 7, 2018, 5:46 PM Hosein Geraili Daronkola <geraili.hsn.gmail.com
wrote:
> Do you know the reason, or keeping which one is appropriate?
>
> On Fri 7. Dec 2018 at 20:45, Brian Radak <brian.radak.gmail.com> wrote:
>
> > fswitch is, in certain ways, incompatible with a long-range correction.
> > I've not seen a published method that combines the two. That being said,
> I
> > implemented one such combination in NAMD, although it has some
> unappealing
> > characteristics with regards to energy conservation.
> >
> > On Fri, Dec 7, 2018 at 1:17 PM Hosein Geraili Daronkola <
> > geraili.hsn.gmail.com> wrote:
> >
> > > The problem is "fswitch" !!!
> > > I checked the test runs of AMBER and it seems that they would always
> turn
> > > the dispersion correction off when using fswitch.
> > > Does anybody know the reason?
> > > Best
> > >
> > >
> > > [image: Mailtrack]
> > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > > >
> > > Sender
> > > notified by
> > > Mailtrack
> > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > > >
> > > 12/07/18,
> > > 7:14:55 PM
> > >
> > > On Fri, Dec 7, 2018 at 4:55 PM Hosein Geraili Daronkola <
> > > geraili.hsn.gmail.com> wrote:
> > >
> > > > By the way, I am using periodic boundary conditions.
> > > >
> > > >
> > > > [image: Mailtrack]
> > > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > >
> > > Sender
> > > > notified by
> > > > Mailtrack
> > > > <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > >
> > > 12/07/18,
> > > > 4:54:54 PM
> > > >
> > > > On Fri, Dec 7, 2018 at 3:58 PM Hosein Geraili Daronkola <
> > > > geraili.hsn.gmail.com> wrote:
> > > >
> > > >> Hi,
> > > >> I am using vdwmeth = 1, in amber18, but in the output file it is 0.
> > > >>
> > > >> even if I don't assign it, it is still zero. Both sander and pmemd
> of
> > > >> amber18.
> > > >>
> > > >> What is the problem?
> > > >> Best regards
> > > >>
> > > >>
> > > >> [image: Mailtrack]
> > > >> <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > >
> > > Sender
> > > >> notified by
> > > >> Mailtrack
> > > >> <
> > >
> >
> https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&
> > >
> > > 12/07/18,
> > > >> 3:56:15 PM
> > > >>
> > > >
> > > >
> > > > --
> > > > Hosein Geraili Daronkola
> > > > Ph.D. student,
> > > >
> > > > Wissenschaftspark Potsdam-Golm
> > > > Max Planck Institute of Colloids and Interfaces
> > > > Theory and Bio-Systems Department
> > > >
> > > > Office K-1.119
> > > > Am Mühlenberg 1 OT Golm
> > > > 14476 Potsdam
> > > > Germany
> > > >
> > > > Phone: +49-(0)331 567-9611
> > > > Fax: +49-(0)331 567-9602
> > > > E-mail: hosein.geraili.mpikg.mpg.de
> > > >
> > > >
> > >
> > > --
> > > Hosein Geraili Daronkola
> > > Ph.D. student,
> > >
> > > Wissenschaftspark Potsdam-Golm
> > > Max Planck Institute of Colloids and Interfaces
> > > Theory and Bio-Systems Department
> > >
> > > Office K-1.119
> > > Am Mühlenberg 1 OT Golm
> > > 14476 Potsdam
> > > Germany
> > >
> > > Phone: +49-(0)331 567-9611
> > > Fax: +49-(0)331 567-9602
> > > E-mail: hosein.geraili.mpikg.mpg.de
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> Hosein Geraili Daronkola
> Ph.D. student,
>
> Wissenschaftspark Potsdam-Golm
> Max Planck Institute of Colloids and Interfaces
> Theory and Bio-Systems Department
>
> Office K-1.119
> Am Mühlenberg 1 OT Golm
> 14476 Potsdam
> Germany
>
> Phone: +49-(0)331 567-9611
> Fax: +49-(0)331 567-9602
> E-mail: hosein.geraili.mpikg.mpg.de
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Dec 08 2018 - 07:30:02 PST
