Dear Bill and Hirdesh,
Thanks for your answers.
------------------------------------------------------------------------------------
> One possible cause is your md run terminated abnormally,
> and the file wasn't closed properly.
I think my md run terminated normally. I checked out file.
The last lines of *.out file is as follows:
NSTEP = 124500 TIME(PS) = 499.000 TEMP(K) = 298.18 PRESS =
-176.7
Etot = -65262.0193 EKtot = 15940.4014 EPtot =
-81202.4207
BOND = 365.2658 ANGLE = 980.2199 DIHED =
1366.8696
1-4 NB = 497.6672 1-4 EEL = 6505.0888 VDWAALS =
10080.3169
EELEC = -101291.1620 EHBOND = 0.0000 RESTRAINT =
293.3131
EAMBER (non-restraint) = -81495.7338
EKCMT = 7259.0752 VIRIAL = 8267.5567 VOLUME =
264293.2688
Density =
1.0123
Ewald error estimate: 0.7382E-04
------------------------------------------------------------------------------
NSTEP = 125000 TIME(PS) = 500.000 TEMP(K) = 298.19 PRESS =
-156.0
Etot = -65398.9097 EKtot = 15941.0525 EPtot =
-81339.9622
BOND = 379.7711 ANGLE = 1002.1907 DIHED =
1377.5799
1-4 NB = 521.4173 1-4 EEL = 6560.2145 VDWAALS =
10300.7243
EELEC = -101703.6723 EHBOND = 0.0000 RESTRAINT =
221.8124
EAMBER (non-restraint) = -81561.7746
EKCMT = 7231.8712 VIRIAL = 8121.2591 VOLUME =
264040.5970
Density =
1.0133
Ewald error estimate: 0.1052E-03
------------------------------------------------------------------------------
A V E R A G E S O V E R 125000 S T E P S
NSTEP = 125000 TIME(PS) = 500.000 TEMP(K) = 297.94 PRESS =
-20.1
Etot = -65390.3722 EKtot = 15927.6308 EPtot =
-81318.0030
BOND = 376.8976 ANGLE = 1011.5016 DIHED =
1354.7631
1-4 NB = 502.2655 1-4 EEL = 6567.3328 VDWAALS =
10432.8994
EELEC = -101852.7566 EHBOND = 0.0000 RESTRAINT =
289.0934
EAMBER (non-restraint) = -81607.0964
EKCMT = 7242.5865 VIRIAL = 7372.5524 VOLUME =
270076.2360
Density =
0.9930
Ewald error estimate: 0.6881E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 125000 TIME(PS) = 500.000 TEMP(K) = 1.82 PRESS =
136.7
Etot = 341.0877 EKtot = 97.1201 EPtot =
322.3445
BOND = 15.8723 ANGLE = 23.5151 DIHED =
11.2848
1-4 NB = 8.6743 1-4 EEL = 19.5114 VDWAALS =
124.8683
EELEC = 368.7763 EHBOND = 0.0000 RESTRAINT =
11.2008
EAMBER (non-restraint) = 311.1437
EKCMT = 65.2301 VIRIAL = 810.3381 VOLUME =
13905.0957
Density =
0.0451
Ewald error estimate: 0.5150E-04
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
|>>>>>>>>PROFILE of Average TIMES>>>>>>>>>
| Build the list 981.21 (89.09% of List )
| Other 120.15 (10.91% of List )
| List time 1101.36 (12.82% of Nonbo)
| Short_ene time 5693.01 (95.23% of Direc)
| Other 284.95 ( 4.77% of Direc)
| Direct Ewald time 5977.96 (79.79% of Ewald)
| Adjust Ewald time 32.90 ( 0.44% of Ewald)
| Fill Bspline coeffs 119.17 (11.12% of Recip)
| Fill charge grid 145.16 (13.54% of Recip)
| Scalar sum 153.82 (14.35% of Recip)
| Grad sum 240.82 (22.47% of Recip)
| FFT back comm time 77.08 (19.95% of FFT t)
| Other 309.36 (80.05% of FFT t)
| FFT time 386.44 (36.05% of Recip)
| Other 26.50 ( 2.47% of Recip)
| Recip Ewald time 1071.92 (14.31% of Ewald)
| Force Adjust 333.21 ( 4.45% of Ewald)
| Virial junk 67.24 ( 0.90% of Ewald)
| Other 8.79 ( 0.12% of Ewald)
| Ewald time 7492.22 (87.18% of Nonbo)
| Nonbond force 8593.86 (98.01% of Force)
| Bond/Angle/Dihedral 38.21 ( 0.44% of Force)
| FRC Collect time 78.46 ( 0.89% of Force)
| Other 58.08 ( 0.66% of Force)
| Force time 8768.61 (79.98% of Runmd)
| Shake time 45.14 ( 0.41% of Runmd)
| Verlet update time 1712.21 (15.62% of Runmd)
| Ekcmr time 125.75 ( 1.15% of Runmd)
| CRD distribute time 57.81 ( 0.53% of Runmd)
| Other 253.78 ( 2.31% of Runmd)
| Runmd Time 10963.29 (100.0% of Total)
| Other 0.58 ( 0.01% of Total)
| Total time 10963.88 (100.0% of ALL )
| Number of list builds : 13502
| Highest rstack allocated: 277853
| Highest istack allocated: 6097
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 10963.45 Per Step(ms) = 87.71
| ns/day = 1.97 seconds/ns = 43853.80
| -----------------------------------------------------
| Job began at 22:49:08.508 on 09/23/2016
| Setup done at 22:49:09.098 on 09/23/2016
| Run done at 01:51:52.526 on 09/24/2016
| wallclock() was called 7152267 times
-----------------------------------------------------------------------------------
> Do not select "amber coordinates with periodic condition" option. After
> loading parameter file, load the netcdf file as "automatically file type".
I did what you said, but VMD says " Please select a type file"
-------------------------------------------------------------------------------------
How to fix this issue?
Best,
Andrew
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Received on Sun Sep 25 2016 - 00:30:02 PDT
