[obasekia]

Good day all, i tried to equilibrate my structure and i got an error about Shake algorithm failed to converge . i tired including the shake_iteration to  VALUE OF 2000 but the error still persist

Update_Num_Deg_Freedom> Number of degrees of freedom was updated
num_deg_freedom = 526106 (After setup of SHAKE/RATTLE)
Update_Num_Deg_Freedom> Number of degrees of freedom was updated
num_deg_freedom = 269562 (Group temperature/pressure case)
[STEP4] Compute Single Point Energy for Molecules
STEP BOND ANGLE UREY-BRADLEY DIHEDRAL IMPROPER CMAP VDWAALS ELECT RESTRAINT_TOTAL
————— ————— ————— ————— —————
0 1226.9470 5199.5045 580.1852 13780.5099 213.3866 -539.5444 13800394.6276 -1033002.6222 0.0001
[STEP5] Perform Molecular Dynamics Simulation
Initial_Velocity> Generate initial velocities
iseed = 670355
temperature = 300.000
Random_Init_Velocity> Initialize the random number
seed = 670355
Compute_Shake> SHAKE algorithm failed to converge: indexes 13315 13316
Compute_Shake> SHAKE algorithm failed to converge: indexes 11343 11344 11345 11346
Compute_Shake> SHAKE algorithm failed to converge: indexes 11082 11083
Compute_Shake> SHAKE algorithm failed to converge: indexes 2974 2975 2976
Compute_Shake> SHAKE algorithm failed to converge: indexes 13726 13727
Compute_Shake> SHAKE algorithm failed to converge: indexes 1962 1963
Compute_Shake> SHAKE algorithm failed to converge: indexes 1958 1959
Compute_Shake> SHAKE algorithm failed to converge: indexes 10784 10785
Compute_Shake> SHAKE algorithm failed to converge: indexes 10790 10791 10792 10793
1005,1 Bot

 

 

[ckobayashi]

Hello.

Shake failures are most often caused by other factors (in-sufficient minimization, bad initial structures, and/or inappropriate input parameters), not by insufficient shake_iteration. (The default value would be sufficient.)

You can find the issue in troubleshooting (chapter 12) of the user manual.

 

Kobayashi

[ckobayashi]

Sorry, troubleshooting is given in chapter 22. (page 150 of GENESIS 2.0 user guide)