Vakues of various flags are printed in the output file even if you did not
set them.
On Mon, Sep 4, 2023, 7:36 AM Kankana Bhattacharjee via AMBER <
amber.ambermd.org> wrote:
> Hello,
>
> I ran the constant pressure equilibration by following the ras-raf mmpbsa
> amber tutorial (without the press0 keyword). Will it take the by default "1
> bar" ya explicitly have to mention "press0" keyword in input file ?
>
> Thanks
> Kankana Bhattacharjee
>
>
>
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> 09/04/23,
> 05:00:48 PM
>
> On Mon, Sep 4, 2023 at 4:12 PM Dr. Anselm Horn via AMBER <
> amber.ambermd.org>
> wrote:
>
> > Kankana,
> >
> > you are right, the input variable 'pres0' controls the pressure (cf
> > Amber23 manual, section 21.6.8 "Pressure regulation")´, and the default
> > is 1.0.
> >
> > You can verify the pressure value used by Amber in a simulation by
> > inspecting the output file, where at the beginning, after your input has
> > been repeated, the settings for the simulations are printed.
> > "Pressure regulation" is a separate subsection.
> >
> > Good luck,
> >
> > Anselm
> >
> > Bioinformatik | NHR.FAU
> > Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> > Germany
> >
> >
> >
> > Am 02.09.2023 um 14:50 schrieb Kankana Bhattacharjee via AMBER:
> > > Thanks a lot !!
> > > But, to set pressure at 1 bar, which keyword will work ? As I exactly
> > > followed the RAS-RAF mmpbsa tutorial, but which keyword is controlling
> > the
> > > pressure at 1 bar ?
> > > Is it "press0=1", I dint find any tutorial where the pressure value is
> > > explicitly mentioned. Kindly let me know about this.
> > >
> > >
> > >
> > >
> > > [image: Mailtrack]
> > > <
> >
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> > > 09/02/23,
> > > 06:07:19 PM
> > >
> > > On Sat, Sep 2, 2023 at 5:12 PM Nikolay N. Kuzmich <nnkuzmich.gmail.com
> >
> > > wrote:
> > >
> > >> Hi Kankana,
> > >> yes, ntp=1 means simulation with constant pressure and isotropic
> > pressure
> > >> scaling
> > >> which should suit your type of simulation (unless no membrane
> present).
> > >> You can also check the Amber23 manual for more details.
> > >> Kind regards
> > >> Nick
> > >>
> > >>
> > >> сб, 2 сент. 2023 г. в 09:35, Kankana Bhattacharjee via AMBER <
> > >> amber.ambermd.org>:
> > >>
> > >>> Dear AMBER users,
> > >>>
> > >>> I have query regarding the NPT equilibration keyword, I followed the
> > >>> keywords which is mentioned in the RAS-RAF tutorial (density.in,
> > >>> equil.in).
> > >>> To perform simulation at 1 bar, which keyword is appropriate ? Is it
> > >>> "ntp=1" ? I am sharing the "equil.in" file and used the same input
> > file
> > >>> for
> > >>> my protein-ligand complex simulation. Kindly suggest me.
> > >>> heat ras-raf
> > >>> &cntrl
> > >>> imin=0,irest=1,ntx=5,
> > >>> nstlim=250000,dt=0.002,
> > >>> ntc=2,ntf=2,
> > >>> cut=8.0, ntb=2, ntp=1, taup=2.0,
> > >>> ntpr=1000, ntwx=1000,
> > >>> ntt=3, gamma_ln=2.0,
> > >>> temp0=300.0, ig=-1,
> > >>>
> > >>> Thanks & Regards
> > >>> Kankana Bhattacharjee
> > >>> Ph.D. Scholar
> > >>> Department of Chemistry
> > >>> Ashoka University
> > >>> Sonipat, Haryana
> > >>> _______________________________________________
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> > >>>
> > >>
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Received on Mon Sep 04 2023 - 05:00:03 PDT
