Dear AMBER developers and users,
I recently encountered an issue when using sander with imin=5 to extract energy from a trajectory. Specifically, I observed that sander.MPI produced different nonbonded energy values when different numbers of processes were used. For example:
With mpirun -np 4:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3656E+05 1.6835E+01 1.3896E+02 O 34549
BOND = 684.2128 ANGLE = 1452.6058 DIHED = 1207.5225
VDWAALS = 20144.5207 EEL = -172841.5000 HBOND = 0.0000
1-4 VDW = 1038.9863 1-4 EEL = 11518.6327 RESTRAINT = 0.0000
CMAP = 239.2315
minimization completed, ENE= -.13655579E+06 RMS= 0.168353E+02
|Largest sphere to fit in unit cell has radius = 31.533
With mpirun -np 8:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3653E+05 1.6819E+01 1.1655E+02 CG 3132
BOND = 684.2128 ANGLE = 1452.6058 DIHED = 1207.5225
VDWAALS = 20145.8189 EEL = -172818.4430 HBOND = 0.0000
1-4 VDW = 1038.9863 1-4 EEL = 11518.6327 RESTRAINT = 0.0000
CMAP = 239.2315
minimization completed, ENE= -.13653143E+06 RMS= 0.168189E+02
|Largest sphere to fit in unit cell has radius = 31.533
However, when I set imin=1 for structure optimization, the results from np=4 and np=8 showed only minor energy differences, with each term varying by no more than 0.001, while GMAX remained identical. This suggests that the issue is specific to trajectory analysis. Given that the differences in energy and gradients are not negligible, I suspect that there might be an issue in the trajectory analysis implementation of sander.MPI.
I would appreciate any insights or suggestions regarding this behavior. Thank you for your time and help.
Best regards,
Yunhao Mei
College of Chemistry and Chemical Engineering
Peking University
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Received on Thu Mar 20 2025 - 05:00:02 PDT
