Hi,
The 'align' command is rotating the coordinates, which affects how the
force vectors are pointing. I'm guessing if you take away the 'align'
command the forces will match.
-Dan
On Wed, Feb 24, 2021 at 7:10 PM Click, Timothy Howard
<tclick.alumni.ou.edu> wrote:
>
> Salutations. I am attempting to calculate the forces between two atoms (Na+ and Cl-) in vacuo, and when I ran sander on a production run, I output forces. I also opted to postprocess using cpptraj
>
> parm nacl.parm7
> trajin production.nc
> align mass first
> esander production out forces.csv saveforces igb 6
> trajout forces.trj mdfrc
>
> However, the values differ
>
> sander:
> array([[ 0.0828545 , -0.18094742, -0.03403379],
> [-0.0828545 , 0.18094742, 0.03403379]], dtype=float32)
>
> cpptraj:
> array([[-0.037, 0.081, 0.015],
> [ 0.037, -0.081, -0.015]], dtype=float32)
>
> I am also attempting to calculate the values manually using Python. The energies are identical (sander output file == cpptraj == Python). In Python, I used the basic energy equation as noted in the seminal paper (Cornell, 1995). I have attempted to look in the code ($AMBERHOME/AmberTools/src/mdgx/NBOnlyLJ.c and ($AMBERHOME/AmberTools/src/mdgx/NBLoop.c), but I am still confused on the calculations.
>
> Thanks for your help.
> ——
> Cordially,
> 柯明 Timothy H. Click, Ph.D.
> College of Veterinary Medicine
> 107 Math Sciences
> Oklahoma State University
> Stillwater, OK 74078
>
>
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Received on Thu Feb 25 2021 - 03:00:02 PST
