As a user of orca, I would also like to address that the input file for
orca specified a 'maxcore 30000'. You should be carefull about not
allocating more physical memory than present in your system. Setting
maxcore to 30000 indicates that you are gathering 30GB of RAM per CPU
thread that you employ. The total amount of RAM in your system should
therefore be 240GB, which is more than your usual workstation.
Kind regards
Charles-Alexandre Mattelaer
Op 1 mrt. 2018 10:46 a.m. schreef "minyuan.mail.ustc.edu.cn" <
minyuan.mail.ustc.edu.cn>:
> Hi Andy,
>
> Set num_threads to either 1 or 8, fullpath/orca inputfile.inp >
> output.out, seccessfully completed.
> The orca runs only using the full path, thougth I have added its path in
> ~/.bashrc.
> If using command: orca inputfile.inp > output.out, message comes as,
> /usr/lib/python3/dist-packages/pyatspi/__init__.py:17: PyGIWarning: Atspi
> was imported without specifying a version first. Use
> gi.require_version('Atspi', '2.0') before import to ensure that the right
> version gets loaded.
> from gi.repository import Atspi
>
> I'M confused.
>
> BestWishes,
> Yuan Min
>
>
> minyuan.mail.ustc.edu.cn
>
> From: Goetz, Andreas
> Date: 2018-03-01 16:25
> To: AMBER Mailing List
> Subject: Re: [AMBER] AMBER/ORCA for QM/MM
> You are not giving us enough information to debug your problem. Have a
> look at the Orca output file. This should give you more information on what
> went wrong. Also, it is a good idea to first make sure that everything
> works as expected with the serial version.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Mar 1, 2018, at 12:09 AM, minyuan.mail.ustc.edu.cn wrote:
> >
> > Hi, Andy
> >
> > Thank you for your reply. It started to run after removing chagre in
> &orc namelist.
> > But it failed again.
> > ************************************************************
> **********************************************
> > The orc_job.engrad file is empty, thus the corresponding message is:
> > 4. RESULTS
> > ------------------------------------------------------------
> --------------------
> > SANDER BOMB in subroutine read_results (qm2_extern_orc_module)
> > Error reading Orca output from file orc_job.engrad
> > (Current total energy or gradient not found or unsupported units.)
> >
> > ************************************************************
> ***************************************************************
> > The orc_job.inp file is:
> > # Run using SANDER file-based interface for Orca
> > #
> > %pal nprocs 8 end
> > !blyp SVP verytightscf
> > %method
> > grid 4
> > finalgrid 6
> > end
> > %scf
> > maxiter 100
> > end
> > %MaxCore 30000
> > ! ENGRAD
> > ! Angs NoUseSym
> > %pointcharges "ptchrg.xyz"
> > *xyzfile 0 1 inpfile.xyz
> >
> > ************************************************************
> *************************************************
> > It seems that orca doesn't work.
> >
> > Looking forward to hear your help.
> >
> > BestWishes,
> > Yuan Min
> >
> >
> > minyuan.mail.ustc.edu.cn
> >
> > From: Goetz, Andreas
> > Date: 2018-03-01 12:10
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] AMBER/ORCA for QM/MM
> > Charge and spin need to be specified only in the &qmmm namelist, see the
> error message:
> >
> > SANDER BOMB in subroutine get_namelist (qm2_extern_orc_module)
> > The charge and spin keywords are deprecated
> > Please specify charge (qmcharge) and spin multiplicity (spin) in the
> &qmmm namelist.
> >
> > All the best,
> > Andy
> >
> > Sent from my iPhone
> >
> > On Feb 28, 2018, at 19:24, "minyuan.mail.ustc.edu.cn<mailto:
> minyuan.mail.ustc.edu.cn>" <minyuan.mail.ustc.edu.cn<mailto:
> minyuan.mail.ustc.edu.cn>> wrote:
> >
> > Hi,
> >
> > My QM/MM calculations failed using amber/orca.
> > The prmtop and crd files come from the online tutorial
> http://ambermd.org/tutorials/advanced/tutorial2/section3.htm.
> > ************************************************************
> *******************************************************
> > My workstations: 16 CPU, one GPU, single computer, openmpi
> > ************************************************************
> *******************************************************
> > Here is the input file:
> > Initial min of our structure QMMM
> > &cntrl
> > imin=1, maxcyc=500, ncyc=200,
> > cut=8.0, ntb=1, ntc=2, ntf=2,
> > ifqnt=1
> > /
> > &qmmm
> > qmmask=':1-2',
> > qmcharge=0,
> > spin=1,
> > qm_theory='EXTERN',
> > qmshake=1,
> > qm_ewald=0
> > /
> > &orc
> > method='blyp',
> > basis='svp',
> > charge=0
> > /
> >
> > ************************************************************
> *****************************************************************
> > Here is the QM part in output file:
> > 3.1 QM CALCULATION INFO
> > ------------------------------------------------------------
> --------------------
> > | !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> > | Not all MPI implementations fully support system calls that execute
> > | MPI parallel programs. In this case it will not be possible to run
> > | MPI parallel versions of both sander and the external QM program.
> > | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >
> > | Please also cite the following work for the use of the QM/MM interface:
> >
> > | A. W. G"otz, M. A. Clark, R. C. Walker
> > | "An extensible interface for ab initio QM/MM molecular dynamics
> simulations
> > | with AMBER"
> > | J. Comput. Chem. 35 (2014) 95-108.
> > | DOI: 10.1002/jcc.23444
> >
> > Constants for unit conversion taken from
> > Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
> > and using the thermochemical calorie (1 cal = 4.184 J):
> >
> > A_TO_BOHRS = 1.889726132873E+00
> > AU_TO_KCAL = 6.2750946943E+02
> > AU_TO_DEBYE = 2.54174623E+00
> >
> > Running QM calculation with Orca <<<
> >
> > SANDER BOMB in subroutine get_namelist (qm2_extern_orc_module)
> > The charge and spin keywords are deprecated
> > Please specify charge (qmcharge) and spin multiplicity (spin) in the
> &qmmm namelist.
> >
> > ************************************************************
> ********************************************************
> > Here is the message in command line:
> > :~/orca/projects/NMA$ mpirun -np 8 sander.MPI -O -i min_qmmm.in -o
> min_qmmm.out -p NMA.prmtop -c NMA.inpcrd -r min_qmmm.rst
> > ------------------------------------------------------------
> --------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> > ************************************************************
> *************************************************************
> >
> > How to solve this problem?
> > Looking forward to hear your help.
> >
> > BestWishes,
> > Yuan Min
> >
> >
> > minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>
> >
> > From: Goetz, Andreas
> > Date: 2018-02-27 05:04
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] AMBER/ORCA for QM/MM
> > The interface will work with Orca versions 3 (e.g. 3.0.3) and 4 (e.g.
> 4.0.2). See also previous messages on this mailing list
> http://archive.ambermd.org/201707/0486.html
> >
> > Link atoms work exactly as with the built-in semiempirical and DFTB
> methods. They will be added automatically if your QM/MM boundary crosses
> covalent bonds. Make sure to cut only across single bonds and not across
> polar bonds, i.e. C-C single bonds typically are appropriate. See also the
> Amber manual.
> >
> > All the best,
> > Andy
> > ―
> > Dr. Andreas W. Goetz
> > Assistant Research Scientist
> > San Diego Supercomputer Center
> > Tel: +1-858-822-4771
> > Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
> > Web: www.awgoetz.de<http://www.awgoetz.de>
> >
> > On Feb 26, 2018, at 6:24 AM, minyuan.mail.ustc.edu.cn<mailto:
> minyuan.mail.ustc.edu.cn> wrote:
> >
> > Hi,
> >
> > I want to use AMBER/ORCA to achieve QM/MM calculations.
> > Which version of ORCA program is supported by AMBER16?
> >
> > For tutorial I only find one in which boundaries of QM an MM atoms are
> not involved.
> > How to deal with the QM-MM boundary if they are linked via covalent
> bonds?
> >
> > Looking forward to hear your reply.
> >
> > BestWishes,
> > YuanMin
> >
> >
> > minyuan.mail.ustc.edu.cn<mailto:minyuan.mail.ustc.edu.cn>
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Received on Thu Mar 01 2018 - 02:00:03 PST
