Hi Manuele,
I will change the code for inclusion with AmberTools 20 and send you a patch for AmberTools 19. I should be able get to it over the weekend.
If you know Fortran and want to try yourself, have a look at $AMBERHOME/AmberTools/src/sander/qm2_extern_orc_module.F90. Search for the comment line “! Backup old input and datfiles”, and modify the lines that follow to keep the datfile. Variable nstep contains the current MD step number.
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 Feb 13, 2020, at 6:25 AM, emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> Dear Andreas,
>
> Thanks for helping out. I really would like to do it.
> So, I installed AmberTool19, how should I modify the source file to keep
> ORCA output for each step ?
> Also, how can I access to the source code in this case?
>
> Regards,
> Manuele
>
>
> Il giorno gio 13 feb 2020 alle ore 10:21 Goetz, Andreas <agoetz.sdsc.edu>
> ha scritto:
>
>> Dear Manuele,
>>
>> Currently only the dipole moment is read from Orca output files along the
>> trajectories.
>>
>> With minor modifications to the source code you could keep Orca output
>> files for every step or every n-th step and then post-process these files.
>> I would recommend moving to AmberTools 19. Let me know if you want to try
>> and I can help you modify the source code. I also put this onto my Todo
>> list for suggested features in future releases.
>>
>> 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 Feb 13, 2020, at 1:21 AM, emanuele falbo <falbo.emanuele.gmail.com>
>> wrote:
>>>
>>> Dear users,
>>>
>>> Since during the QM/MM calculations ORCA overwrites for every step its
>>> output files, I am forced to rerun QM single points to compute properties
>>> like HOMO, LUMO, and etc. in every step.
>>>
>>> Besides the energies, I wonder if there is any way to let Amber output
>>> other properties of the QM regions in the Amber output file ? ( I am
>> using
>>> Amber14). Thanks for the help.
>>>
>>> Regards,
>>> Manuele
>>>
>>> --
>>>
>>> *Emanuele Falbo*
>>> PhD student
>>> Penfold group
>>> School of Natural and Environmental Sciences
>>> Bedson Building, Newcastle University
>>> Newcastle upon Tyne, NE1 7RU
>>> w: http://tompenfoldresearch.weebly.com/
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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>>
>
>
> --
>
> *Emanuele Falbo*
> PhD student
> Penfold group
> School of Natural and Environmental Sciences
> Bedson Building, Newcastle University
> Newcastle upon Tyne, NE1 7RU
> w: http://tompenfoldresearch.weebly.com/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Feb 13 2020 - 23:30:02 PST
