Dear Ge Song,
If this is from a QM/MM calculation, then the difference in forces is due to Lennar-Jones interactions.
If you add “debug = 2,” to your &gau namelist, then the QM/MM interface will print the converted energy in kcal/mol and forces in kcal/mol/Angstrom to mdout. This should match with the numbers that you converted manually as it does not contain LJ energy or forces. In a pure QM calculation (no MM atoms) the forces should match with the content of the mdfrc file.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Nov 10, 2024, at 5:57 PM, Ge Song via AMBER <amber.ambermd.org> wrote:
Dear Amber community,
I am running single point QM/MM in Sander with forces being output. The calculation finished normally, and the energy from the gaussian log file and that from the mdout file are consistent according to
https://urldefense.com/v3/__http://archive.ambermd.org/201812/0031.html__;!!Mih3wA!ASmoTRVtoWAjX-zZbgwTGW2sjRB29QG5fnInvrtGLFnlteLbQs_Wx-vZ6A4_VqarXn9HFu3i-kN-NA$ . However, when I also checked the forces, I found they are roughly consistent but significant discrepancies exist:
The forces on the first atom in the gaussian log file (old.gau_job.log) is:
-0.012109279 -0.000859028 -0.003084640
those are in Hartree/Bohr, converting into kcal/mol would be:
-14.359 -1.019 -3.658
While in my mdfrc file, they are:
-14.517 -0.793 -3.978
So, they look similar, but I don't think these errors are neglectable.
I have tried both Amber19 and Amber22, and they gave the same results. Here is my input setting of sander:
Production
&cntrl
imin=5,
ntx=5,
irest=1,
temp0=300.0,
cut=9999.0,
ntb=0,
ntwx=1,
ntwf=1,
ioutfm=0,
ifqnt=1
/
&qmmm
qmmask=':1-3',
qm_theory='EXTERN',
qmcharge=0,
spin=1,
qmshake=0,
qm_ewald=0, qm_pme=0,
/
&gau
num_threads = 16,
mem='16GB',
use_template=1,
/
And the command line I was using:
mpirun -np 4 sander.MPI -O -i qmmm_rerun.in -o qmmm_rerun.out -p ala_amber.top -c amber_heat.ncrst -y amber_md_frame1.nc -frc mdfrc
Ge Song
Personal Academic Website of Ge - Physics of Life<
https://urldefense.com/v3/__https://calvinge.github.io/gesong.github.io/__;!!Mih3wA!ASmoTRVtoWAjX-zZbgwTGW2sjRB29QG5fnInvrtGLFnlteLbQs_Wx-vZ6A4_VqarXn9HFu2ohTHtjQ$ >
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Received on Sun Nov 10 2024 - 19:00:02 PST
