PBSA WARNING: in MG: SOR maxitn exceeded!

Bejo Ropii

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Sep 10, 2021, 9:54:41 AM9/10/21

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Hi, I am performing binding energy in parallel calculation using gmx_MMPBSA for double-stranded nucleic acid using single trajectories approach but I got this error in _GMXMMPBSA_complex_pb.mdout :

FINAL RESULTS

NSTEP ENERGY RMS GMAX NAME NUMBER

1 -6.8404E+03 2.0168E+01 1.2568E+02 C2 361

BOND = 648.4845 ANGLE = 1213.8277 DIHED = 2191.0145

UB = 446.7374 IMP = 28.3123 CMAP = 0.0000

VDWAALS = -1108.8371 EEL = 20014.0508 EPB = -29442.3551

1-4 VDW = 1152.0338 1-4 EEL = -2127.0757 RESTRAINT = 0.0000

ECAVITY = 1293.4855 EDISPER = -1150.1028

minimization completed, ENE= -.68404242E+04 RMS= 0.201676E+02

minimizing coord set # 3

PBSA WARNING: in MG: SOR maxitn exceeded!

this is my input

mmpbsa.in

&general

sys_name="WB_amp",

startframe=4701, endframe=5000, verbose=2,

interaction_entropy=1, ie_segment=25, temperature=300

/

&pb

# radiopt=0 is recommended which means using radii from the prmtop file

# for both the PB calculation and for the NP calculation

istrng=0.0, fillratio=4.0, radiopt=0, linit=10000

/

&gb

igb=2, saltcon=0.0,

/

Do I need to set the linit value to be higher?

Thanks

marioe911116

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Sep 10, 2021, 1:31:47 PM9/10/21

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Seems like the iteration convergence criterion (default = 0.001) hasn't been achieved... As you suggested, try to increase the "linit" value and rerun few frames again (preferably the frames around the one is giving problems now) and see how it goes...

cheers!

Bejo Ropii

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Sep 11, 2021, 2:18:13 PM9/11/21

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Hi. I have increased the "linit" value up to 10^12 and it gave another error.

I have performed 50ns MD simulation and got 5002 frames, I have tried to use several number of frames (e.g 10, 100, 250, 300) from several combinations of the frame range (e.g 1-1000, 1001-5000, 4001-5000) but so far the calculation only works for performing 10 frames. The error happens on the 6th or 7th frame in each pb.mdout (I used -np 5 flag).

marioe911116

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Sep 12, 2021, 5:24:09 PM9/12/21

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Hello there! can you send around the files you are using? thus, I can check and see if I find what's going on... in the trajectory file, just include 10 frames and make sure to include those around the one giving the error

cheers!

Mario E.

marioe911116

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Sep 15, 2021, 12:00:58 AM9/15/21

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The convergence criteria in PB calculations might not be satisfied when the trajectory file is not properly fitted... check this session (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/Q%26A/calculations/#possible-solutions) on how to proceed for removing PBC conditions and fitting the trajectory file

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