Hi Emanuele,
Thank you for the feedback. Good to know that you got this working.
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 19, 2020, at 8:27 AM, emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> Hi Andreas,
>
> Thank you very much for the help. I modified the source code, and I am now
> able to keep the ORCA output files.
>
> Kind regards,
> Manuele
>
> Il giorno ven 14 feb 2020 alle ore 07:07 Goetz, Andreas <agoetz.sdsc.edu>
> ha scritto:
>
>> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>>
>>> *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 Wed Feb 19 2020 - 09:30:01 PST
