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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> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Mon Sep 04 2023 - 04:00:03 PDT
