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
> --------------------------------------
>
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Received on Sun Jul 02 2023 - 14:30:02 PDT
