PS,
I just finished a testing based on GAFF instead of GAFF2. The job failed
with the same errors..........
On 02/01/2017 08:46 AM, Albert wrote:
> Hi,
>
> I checked both .mdout and .mdinfo file, and I didn't find any errors
> there. The jobs have been finished successfully. I also visualized the
> trajectory, it looks perfectly.
>
> BTW, I introduced GAFF2 instead of GAFF for my ligand. I don't know
> whether this would be the problem? I submitted some MM/PBSA
> calculation job last year using GAFF for the same problem. It finished
> without any problems.....
>
> Thank you very much.
> Albert
>
> Here is my log files:
> ------------------------------
>
> R M S F L U C T U A T I O N S
>
> NSTEP = 500000 TIME(PS) = 4860.000 TEMP(K) = 1.04 PRESS
> = 76.5
> Etot = 364.0853 EKtot = 224.4516 EPtot = 254.2527
> BOND = 28.3011 ANGLE = 36.4852 DIHED = 27.7499
> 1-4 NB = 14.9697 1-4 EEL = 45.0244 VDWAALS =
> 282.8587
> EELEC = 412.5857 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> EKCMT = 134.7580 VIRIAL = 1764.3124 VOLUME = 658.6156
> Density =
> 0.0006
> ------------------------------------------------------------------------------
>
>
> --------------------------------------------------------------------------------
>
> 5. TIMINGS
> --------------------------------------------------------------------------------
>
>
> | NonSetup CPU Time in Major Routines:
> |
> | Routine Sec %
> | ------------------------------
> | Nonbond 2649.18 87.80
> | Bond 0.00 0.00
> | Angle 0.00 0.00
> | Dihedral 0.00 0.00
> | Shake 4.62 0.15
> | RunMD 362.58 12.02
> | Other 1.02 0.03
> | ------------------------------
> | Total 3017.40
>
> | PME Nonbond Pairlist CPU Time:
> |
> | Routine Sec %
> | ---------------------------------
> | Set Up Cit 0.00 0.00
> | Build List 0.00 0.00
> | ---------------------------------
> | Total 0.00 0.00
>
> | PME Direct Force CPU Time:
> |
> | Routine Sec %
> | ---------------------------------
> | NonBonded Calc 0.00 0.00
> | Exclude Masked 0.00 0.00
> | Other 0.66 0.02
> | ---------------------------------
> | Total 0.66 0.02
>
> | PME Reciprocal Force CPU Time:
> |
> | Routine Sec %
> | ---------------------------------
> | 1D bspline 0.00 0.00
> | Grid Charges 0.00 0.00
> | Scalar Sum 0.00 0.00
> | Gradient Sum 0.00 0.00
> | FFT 0.00 0.00
> | ---------------------------------
> | Total 0.00 0.00
>
> | Final Performance Info:
> | -----------------------------------------------------
> | Average timings for last 5000 steps:
> | Elapsed(s) = 30.18 Per Step(ms) = 6.04
> | ns/day = 28.63 seconds/ns = 3018.15
> |
> | Average timings for all steps:
> | Elapsed(s) = 3018.69 Per Step(ms) = 6.04
> | ns/day = 28.62 seconds/ns = 3018.69
> | -----------------------------------------------------
>
> | Setup CPU time: 0.97 seconds
> | NonSetup CPU time: 3017.40 seconds
> | Total CPU time: 3018.37 seconds 0.84 hours
>
> | Setup wall time: 1 seconds
> | NonSetup wall time: 3018 seconds
> | Total wall time: 3019 seconds 0.84 hours
>
> --------
> NSTEP = 495000 TIME(PS) = 4640.000 TEMP(K) = 296.45 PRESS
> = 153.1
> Etot = -278652.6757 EKtot = 65186.6406 EPtot =
> -343839.3163
> BOND = 1194.8585 ANGLE = 3065.1315 DIHED = 4877.7364
> 1-4 NB = 1405.1198 1-4 EEL = 12973.1657 VDWAALS = 45610.9967
> EELEC = -412966.3249 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> EKCMT = 30464.8553 VIRIAL = 26833.8298 VOLUME =
> 1098454.5845
> Density =
> 1.0029
> ------------------------------------------------------------------------------
>
> | Current Timing Info
> | -------------------
> | Total steps : 500000 | Completed : 495000 | Remaining : 5000
> |
> | Average timings for last 10000 steps:
> | Elapsed(s) = 61.56 Per Step(ms) = 6.16
> | ns/day = 28.07 seconds/ns = 3077.80
> |
> | Average timings for all steps:
> | Elapsed(s) = 3049.52 Per Step(ms) = 6.16
> | ns/day = 28.05 seconds/ns = 3080.32
> |
> |
> | Estimated time remaining: 30.8 seconds.
> ------------------------------------------------------------------------------
>
> ligand/19>
>
>
>
>
>
> On 01/31/2017 05:31 PM, Dwight McGee wrote:
>> Hi,
>>
>> Can you open one of the *mdout files generated and see what error is
>> being
>> printed?
>>
>> Thanks,
>> Dwight
>
>
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Received on Wed Feb 01 2017 - 03:30:03 PST
