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 - 00:00:03 PST
