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 - 05:00:03 PDT
