If you wanted the single point energy of the system, set imin=6, ntpr=1, nstlim=0 and look at EPtot (the total potential energy).
When imin=6, ntpr=1, nstlim=1, sander will likely show 2 energies per frame; the first being the potential energy of the coordinates stored in the trajectory file, and the second being the potential energy after 1 step of dynamics. The imin=6 option means: run molecular dynamics departing from each frame in the input trajectory file. I had suggested using imin=6 because the printcharges option is unavailable with imin=5 (run minimization departing from each frame in the input trajectory file). However, the printcharges output will not appear at dynamics step 0 (based on the printing logic in the molecular dynamics code), so I suggested setting nstlim=1 which will run 1 step of dynamics (and thus allow charge printing).
The energies in the mdout file are kcal/mol. Note that – unless you turned periodicity off – the value of XTBESCF contains the internal QM energy and the periodic electrostatics with the MM and QM-image charges. Many QM/MM interfaces evaluate truncated electrostatics rather than full Ewald electrostatics, so a comparison of the numerical values generated from other interfaces will need to take into consideration how the electrostatics are evaluated. As far as I am aware, Sander is the only program that includes an xTB interface with QM/MM Ewald electrostatics.
-Tim
________________________________
From: Niven Singh <niven.singh.duke.edu>
Sent: Friday, May 17, 2024 7:26 PM
To: Timothy Giese <giese025.rutgers.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] printcharges using Amber24 GFN2-xtB method
Hi,
Thanks so much! This prints out mulliken charges for all atoms in the QM region.
I had another question about xTB in Amber24. When the calculation finishes, there's a XTBESCF= ___ (floating point) in the qmmm.out file. Is this a single point energy? And what are the units?
If I use an older version of amber and interface xTB2 with orca, there is a XTBESCF= in qmmm.out but also a FINAL SINGLE POINT ENERGY in old.orc_job.tpl file. Are these two energies related or separate? And are both in hartrees?
I'm assuming the two numbers are related but I'm not sure how.
Thanks so much!
Niven 🙂
________________________________
From: Timothy Giese via AMBER <amber.ambermd.org>
Sent: Wednesday, May 15, 2024 11:51 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] printcharges using Amber24 GFN2-xtB method
The issue being described doesn't appear to be related to GFN2-xTB. The symptom exists when qm_theory is changed to DFTB2, for example. The printcharges=1 output is disabled in runmin.F90 when imin=5. To accomplish your task, you can instead set the following options in &cntrl: "imin=6, ntpr=1, nstlim=1". You should then see output that looks like "Atomic Charges for Step 1 :".
-Tim
> I'm trying to use QM/MM with Amber24 using the GFN2-xtB method for a single point calculation. I'm trying to print out the Mulliken charges so I can see how the program has spread the qm_charge across the QM subsystem but when I set printcharges to 1, I don't see the charges per atom for my subsystem in the output file.
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Received on Mon May 20 2024 - 08:00:02 PDT
