Dear Professor Walker,
I am pleased to write to you to express my most sincere gratitude for
your prompt response to my request and the time you dedicated to attend
to it. I will test the proposed patch shortly.
With my sincerest thanks,
Hector.
El 2023-07-02 18:08, Ross Walker escribió:
> Hi Hector,
>
> Under the explicit caveat that it's been almost 20 years since I
> looked at this code and am taking a quick 30 second look now:
>
> Line 246 of AmberTools/src/sander/qm_mm.F90
>
> if(qmmm_struct%qm_mm_first_call) then
>
> if (qmmm_mpi%commqmmm_master) then
>
> call qm_print_coords(nstep,.true.)
>
> if (abfqmmm_param%abfqmmm /= 1) then
>
> write(6,'(/80("-")/" 3.1 QM CALCULATION INFO",/80("-"))')
>
> end if
>
> end if
>
> end if
>
> It looks like you could probably just comment out the qm_mm_first_call
> if / end if - that would then get you a file called
> qmmm_region.pdb._nstep_ printed on every step. That would be a LOT of
> I/O so you could also add a modulus test for nstep so it prints say
> only every 1000 steps. Something like:
>
> if (qmmm_mpi%commqmmm_master) then
>
> if (mod(nstep,1000)==0) then
>
> call qm_print_coords(nstep,.true.)
>
> if (abfqmmm_param%abfqmmm /= 1) then
>
> write(6,'(/80("-")/" 3.1 QM CALCULATION INFO",/80("-"))')
>
> end if
>
> end if
>
> end if
>
> Recompile and see if that works. - You could also add and if nstep =
> whatever you set nstlim to (you might have to manually add it since I
> don't know if nstlim is in scope within that routine or not) call
> qm_print_coords... to get the final coordinates written out.
>
> All the best
> Ross
>
>> On Jul 2, 2023, at 17:16, Hector A. Baldoni via AMBER
>> <amber.ambermd.org> wrote:
>>
>> Dear Amber developers,
>>
>> I would like to bring the following matter to your attention. During
>> QM/MM simulations using Sander and the independent quantum program
>> (SQM), the qm_print_coords subroutine (developed by Ross Walker)
>> prints the initial coordinates of the QM region, including link
>> atoms. However, there is no option or keyword to print the
>> intermediate or final coordinates of the QM region and its link
>> atoms during or at the end of the simulation.
>>
>> Therefore, I kindly request your assistance. As I am not proficient
>> in Fortran programming, I need guidance or patch to call the
>> qm_print_coords subroutine at each ntwr step for any QM method, and
>> dump them to file.
>>
>> This functionality would be useful for other users, and is crucial
>> for my application, as I use the final coordinates of the QM region
>> and link atoms for post-processing with qtaim. It would be greatly
>> appreciated if you could provide a patch to dump these final
>> coordinates to a file.
>>
>> Thank you for any suggestions or recommendations you can provide.
>>
>> Sincerely,
>>
>> --
>> --------------------------------------
>> Dr. Hector A. Baldoni
>> Profesor Titular (FQByF-UNSL)
>> Investigador Adjunto (IMASL-CONICET)
>> Area de Quimica General e Inorganica
>> Universidad Nacional de San Luis
>> Chacabuco 917 (D5700BWS)
>> San Luis - Argentina
>> hbaldoni at unsl dot edu dot ar
>> Tel.:+54-(0)266-4520300 ext. 6157
>> --------------------------------------
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!D2Hl9PrDuk7Y-n5PXPzGWrDbsbN6l_P-GxL85zqgtnO7Erc1jZQkUu9nMPdefez0U7sHaQhWGdk$
--
--------------------------------------
Dr. Hector A. Baldoni
Profesor Titular (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
I do not define time, space, place, and motion, as being well known to
all.
-- Newton (1642-1726), Principia
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Received on Mon Jul 03 2023 - 06:30:02 PDT
