Hi Andy,
Thank you for your reply.
Do you mean that for geometry optimization, only built-in semiempirical methods can be used, not the interface-based ab initio or DFT methods? For finding transition states, is there any algorithm in amber?
BestWishes,
Yuan Min
minyuan.mail.ustc.edu.cn
From: Goetz, Andreas
Date: 2018-03-03 15:29
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER/ORCA for QM/MM
Yuan,
This is not different from a QM or QM/MM calculation with a built-in method: You have to specify in the &cntrl namelist that you want to perform a geometry optimization (minimization, set imin = 1).
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 2, 2018, at 2:22 AM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>
> Hi Andy,
>
> Thank you.
>
> I noticed that my amber/orca job had run a single point energy calculation of the QM part.
> How to set the &orc namelist for an geometry optimization of the QM part?
>
> Looking forward to hear your help.
>
> BestWishes,
> YUan Min
>> -----原始邮件-----
>> 发件人: "Goetz, Andreas" <agoetz.sdsc.edu>
>> 发送时间: 2018-03-02 10:04:23 (星期五)
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] AMBER/ORCA for QM/MM
>>
>> Hi Yuan,
>>
>> You have to use the same MPI version that you used during compilation. There are exceptions to this rule, but in general this is required.
>>
>> With OpenMPI versions that I tested, it is not possible to run both sander.MPI and Orca in parallel. It is likely that this will fail. You probably have to use the serial sander version. Typically this is not a big issue since the MM computation is much faster than ab inito or DFT QM.
>>
>> 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 5:13 PM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>>>
>>> Hi Andy,
>>>
>>> Thank you for your help.
>>> With Orca3, openmpi-1.6.5, using COMMAND: sander -O -i min_qmmm.in -o min_qmmm.out -p NMA.prmtop -c NMA.inpcrd -r min_qmmm.rst
>>> orca3 runs well.
>>>
>>> Another problem arises: sander.MPI doesn't work. There must be something wrong with openmpi-1.8 (required by Amber16 MPI version). I have installed openmpi-1.8 using the configure script in amber16 and sander.MPI ran well before the openmpi-1.6.5 installation.
>>>
>>> The two versions of openmpi are installed in different files.
>>>
>>> I wander where the default installation file is in the configure script? I want to configure the openmpi-1.8 from its building file and make uninstall. After clearing, install the openmpi-1.8 again.
>>>
>>> Looking forward to hear your help.
>>>
>>> BestWishes,
>>> Yuan Min
>>>
>>>> -----原始邮件-----
>>>> 发件人: "Goetz, Andreas" <agoetz.sdsc.edu>
>>>> 发送时间: 2018-03-01 19:02:35 (星期四)
>>>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>>>> 抄送:
>>>> 主题: Re: [AMBER] AMBER/ORCA for QM/MM
>>>>
>>>> Yuan, this is an Orca question, not related to Amber. The way MPI is implemented in Orca, you have to use the full path when running parallel jobs. This is documented in the Orca manual. You should probably carefully read the Orca manual and make sure that you understand how to use Orca before trying to run QM/MM MD simulations with Amber and Orca.
>>>>
>>>> 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 1:45 AM, minyuan.mail.ustc.edu.cn wrote:
>>>>>
>>>>> 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>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 03 2018 - 17:00:03 PST
