Thanks a lot sir.
Sir I am using amber22. I have seen in the amber22 manual that, QM-MM
simulations can be done through both FBI and API interfaces. Then which
interface should I choose ? Kindly suggest.
On Fri, Jan 3, 2025 at 3:34 AM Goetz, Andreas <awgoetz.ucsd.edu> wrote:
> Dear Kankana,
>
> You have to choose a QM method that is suitable for the scientific
> question that you want to answer.
>
> Yes, you can use the sample input from the manual as a starting point. At
> the very least you have to adjust the selection of QM atoms and QM charge.
> Note that the sample input applies SHAKE constraints to the QM region. If
> this is not what you want then you have to set qmshake = 0 in the qmmm
> namelist and reduce the time step to 1 fs or 0.5 fs.
>
> You can perform QM/MM MD with DFT using QUICK via sander using the
> executables sander or sander.MPI (for CPU) or sander.quick.cuda or
> sander.quick.cuda.MPI (for GPU). See section 10.3 in the Amber 24 manual
> for details.
>
> The executables quick and quick.MPI (for CPU) and quick.cuda and
> quick.cuda.MPI (for GPU) are for HF or DFT calculations with QUICK, not MD
> simulations. For details see section 9 in the Amber 24 manual or the QUICK
> 24.3 online manual at
> https://quick-docs.readthedocs.io/en/24.3.0/user-manual.html
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Associate Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> On Jan 2, 2025, at 3:52 AM, Kankana Bhattacharjee via AMBER <
> amber.ambermd.org> wrote:
>
> Dear Sir,
>
> I have performed the MM simulation of the binary system and then now I want
> to use QM-MM simulation. So, for that what QM method should I use ?
> I have performed till MM equilibration and now want to run production run
> by using QM-MM method. Sir, this is the sample input I found from the
> AMBER22 manual:
> imin=0, nstlim=10000, ! Perform MD for 10,000 steps
> dt=0.002, ! 2 fs time step
> ntt=1, tempi=0.1, temp0=300.0, ! Berendsen temperature control
> ntb=1, ! Constant volume periodic boundaries
> ntf=2, ntc=2, ! Shake hydrogen atoms
> cut=8.0, ! 8 angstrom classical non-bond cut off
> ifqnt=1 ! Switch on QM/MM coupled potential
> /
> &qmmm
> qmmask=':753', ! Residue 753 should be treated using QM
> qmcharge=-2, ! Charge on QM region is -2
> qm_theory='PM3', ! Use the PM3 semi-empirical Hamiltonian
> qmcut=8.0
> /
> Can I use DFT and other basis sets ? And, what is the command line for
> using quick.MPI or quick.cuda.MPI to execute and can I directly use the
> above input after MM equilibration run ?
>
> Kindly give some suggestions.
>
> Thanks &Regards
> Kankana Bhattacharjee
>
>
> On Tue, Dec 24, 2024 at 4:01 AM David A Case <dacase1.gmail.com> wrote:
>
> On Mon, Dec 23, 2024, Kankana Bhattacharjee wrote:
>
> Dear Sir,
>
>
>
> Please send amber-related questions to the mail reflector,
> amber.ambermd.org,
> and not to me personally. That way, many people can see your question and
> try
> to help, and the answers can help others with similar questions. See
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!CcaOWiGuFrYOVhwFGuJ6nVnyH-ylQUoA2WCc4L9A3JoLCFev6abQrGrchmbuDaneBdJTYzQpA5FrcA$
> for information on how to
> subscribe.
>
>
> If I start building up the pyrrol-water system following
> general instruction to do MD in amber say till equilibration and in
> production run I have to use QM region ?
> Then, how additional equilibration can be performed is it after doing
> initial minimisation, heating and equilibration of the MM system and then
> have to do equlibration by turing on "QM" region ?
>
>
> Please don't treat tutorials as strict descriptions. They are general
> guidelines. The basic idea is to do initial equilibration of the system
> (primarily the waters) in MM, since that is much faster than with QM/MM.
>
> The distinction between "equilibration" and "production" is up to you, as
> are the amounts of time needed for each step. Equilibrating a
> small-molecule/water model will generally be much easier and faster than
> a macromolecular system that you will see in the tutorials.
>
> Also, should I have to use Quick QM-MM tool for running QM-MM MD ? If so,
> then can quick do a semiempirical method ?
>
>
> Quick is for density functional (and similar) quantum models. If you are
> interested in semiempirical QM, just use the ones built into AmberTools,
> and
> described in Chapter 8 of the Amber24 Reference Manual. Don't be afraid to
> experiment.
>
> ....dac
>
>
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>
>
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Received on Fri Jan 03 2025 - 09:30:03 PST
