The API interface is recommended. It has better performance.
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 3, 2025, at 9:19 AM, Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
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<mailto: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<
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All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<https://urldefense.com/v3/__http://www.awgoetz.de__;!!Mih3wA!AX1FNs_2o_fb_43Zy3WTMCup0OLaxla102wsjM69rbeMlVlrEaNHdN0nMHA5xHZgO2hb2KjusHOvr0lfVxgkuuq4XG9nOuDg$>
On Jan 2, 2025, at 3:52 AM, Kankana Bhattacharjee via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Dear Sir,
I have performed the MM simulation of the binary system and then now I want
to use QM-MM simulation. So, for that what QM method should I use ?
I have performed till MM equilibration and now want to run production run
by using QM-MM method. Sir, this is the sample input I found from the
AMBER22 manual:
imin=0, nstlim=10000, ! Perform MD for 10,000 steps
dt=0.002, ! 2 fs time step
ntt=1, tempi=0.1, temp0=300.0, ! Berendsen temperature control
ntb=1, ! Constant volume periodic boundaries
ntf=2, ntc=2, ! Shake hydrogen atoms
cut=8.0, ! 8 angstrom classical non-bond cut off
ifqnt=1 ! Switch on QM/MM coupled potential
/
&qmmm
qmmask=':753', ! Residue 753 should be treated using QM
qmcharge=-2, ! Charge on QM region is -2
qm_theory='PM3', ! Use the PM3 semi-empirical Hamiltonian
qmcut=8.0
/
Can I use DFT and other basis sets ? And, what is the command line for
using quick.MPI or quick.cuda.MPI to execute and can I directly use the
above input after MM equilibration run ?
Kindly give some suggestions.
Thanks &Regards
Kankana Bhattacharjee
On Tue, Dec 24, 2024 at 4:01 AM David A Case <dacase1.gmail.com<mailto:dacase1.gmail.com>> wrote:
On Mon, Dec 23, 2024, Kankana Bhattacharjee wrote:
Dear Sir,
Please send amber-related questions to the mail reflector,
amber.ambermd.org<mailto:amber.ambermd.org>,
and not to me personally. That way, many people can see your question and
try
to help, and the answers can help others with similar questions. See
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!CcaOWiGuFrYOVhwFGuJ6nVnyH-ylQUoA2WCc4L9A3JoLCFev6abQrGrchmbuDaneBdJTYzQpA5FrcA$ 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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Received on Fri Jan 03 2025 - 13:30:01 PST
