Could you post us an mdout file ?
On 02/01/2017 12:11 PM, Albert wrote:
> 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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--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Wed Feb 01 2017 - 03:30:03 PST
