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.
> >
> >
> >
> >
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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 - 05:00:02 PDT
