Hi
RESTARTED DUE TO LINMIN FAILURE
This is not an error and needs no fixing. And looking at your FINAL
RESULTS, everything looks fine ok to me.
Best Regards
Elvis
On Sun, 26 Jul 2020 at 17:31, 辛志宏 <xzhfood.njau.edu.cn> wrote:
> Dear all,
>
> I generate prmtop and inpcrd files (with BOX coordinates), and run MM-MD
> successfully, then I processes the periodic boundary of equil outfile using
> cpptraj due to some water molecular running out of box, I extract the last
> frame (499 frames) of the equil pdb outfile as the QM-MM input file, and
> regenerate prmtop and Inpcrd file, but I found that the BOX coordinates in
> the inpcrd file are gone, so , I copy the BOX coordinates from the initial
> inpcrd file to the new one, and run QM-MM using minimization method,
> however, an error occur "... . RESTARTED DUE TO LINMIN FAILURE..." when it
> run 940, 950 and 970 step, the calculation continue and the job can be
> completed, and there is a prompt "Maximum number of minimization cycles
> reached." in the end (1000 step).
> MY questions are:
> (1) How to fix the isse "RESTARTED DUE TO LINMIN FAILURE.",
> (2) Is the end result correct?
>
> Any suggestion will be much appreciate, thank you in advanced.
>
> I read the amberlist to try finding a solution, but fail.
>
>
> The final result information:
>
> FINAL RESULTS
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1000 -2.1398E+06 2.2966E-01 2.3479E+00 O 4518
>
> BOND = 169.6754 ANGLE = 205.7311 DIHED =
> 715.6707
> VDWAALS = -853.2027 EEL = -462140.5995 HBOND =
> 0.0000
> 1-4 VDW = 254.7265 1-4 EEL = 3126.3753 RESTRAINT =
> 0.0000
> EXTERNESCF = -1681235.0114
>
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
>
> --------------------------------------------------------------------------------
>
> | Build the list 0.27 (42.71% of List )
> | Other 0.37 (57.29% of List )
> | List time 0.64 ( 0.21% of Nonbo)
> | Short_ene time 85.69 (90.47% of Direc)
> | Other 9.03 ( 9.53% of Direc)
> | Direct Ewald time 94.72 (31.38% of Ewald)
> | Adjust Ewald time 0.63 ( 0.21% of Ewald)
> | Fill Bspline coeffs 7.16 ( 3.48% of Recip)
> | Fill charge grid 17.53 ( 8.52% of Recip)
> | Scalar sum 80.79 (39.26% of Recip)
> | Grad sum 30.83 (14.98% of Recip)
> | FFT time 68.14 (33.11% of Recip)
> | Other 1.32 ( 0.64% of Recip)
> | Recip Ewald time 205.77 (68.17% of Ewald)
> | Virial junk 0.40 ( 0.13% of Ewald)
> | Other 0.29 ( 0.10% of Ewald)
> | Ewald time 301.84 (99.79% of Nonbo)
> | Nonbond force 302.49 ( 0.10% of Force)
> | Other 290498.79 (100.0% of QMMM )
> | QMMM 290513.69 (99.89% of Force)
> | Force time 290820.07 (100.0% of Runmd)
> | Runmd Time 290820.07 (100.0% of Total)
> | Total time 290832.85 (100.0% of ALL )
>
> | Number of list builds : 2
>
> | Highest rstack allocated: 2181748
> | Highest istack allocated: 35178
> | Job began at 21:43:33.300 on 07/21/2020
> | Setup done at 21:43:33.937 on 07/21/2020
> | Run done at 06:30:46.150 on 07/25/2020
> | wallclock() was called 50064 times
>
> |3D-RISM memory allocation summary
> |Type Maximum Current
> |Integer 0.00000 GB 0.00000 GB
> |Real 0.00000 GB 0.00000 GB
> |Logical 0.00000 GB 0.00000 GB
> |Character 0.00000 GB 0.00000 GB
> |---------------------------------------
> |Total 0.00000 GB 0.00000 GB
>
>
>
>
> my minization file as follows:
>
>
> Initial min of our structure QMMM
> &cntrl
> imin = 1, maxcyc = 1000, ncyc = 600,
> ntx = 1,
> irest = 0,
> ntb = 1,
> cut = 12.0, ntc = 1, ntf = 1,
> ntpr = 10,
> ntwx = 1,
> ibelly = 1,
> bellymask =':1 < .12.0',
> ifqnt = 1,
> &end
> &qmmm
> qmmask=':1,12,15,122,294,295,8573',
> qmcharge = 0,
> spin = 2,
> qm_theory = 'EXTERN',
> qmshake= 0,
> qm_ewald=0, qm_pme=1,
> qmcut = 12.0,
> writepdb= 1
> &end
> &gau
> executable = 'g16',
> method = 'B3LYP',
> basis = '6-31G*',
> num_threads = 20,
> mem = '200GB'
> dipole = 1,
> use_template = 0,
> &end
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Received on Sun Jul 26 2020 - 06:00:05 PDT
