Dear Bill,
I renamed trajectory to end in "*.nc".
About both of *.netcdf and *.nc files, when I load them " Automatically
file type", VMD says " Please select a file type".
About both of *.netcdf and *.nc files, when I load them " AMBER
Coordinates file
type", VMD says " Problem reading CRD files".
About both of *.netcdf and *.nc files, when I load them " AMBER
Coordinates with
Periodic Box file type", VMD says " Problem reading CRD files".
When I drag-to-scroll down the format list, there is not NetCDF.
In my VMD format list, there are following formats related to AMBER:
AMBER Coordinates
AMBER Coordinates with Periodic Box
AMBER Parm
AMBER7 Parm
AMBER7 Restart
Which version of VMD support NetCDF? I use VMD 1.9.1.
Best,
Andrew
On Sun, Sep 25, 2016 at 10:39 AM, Andrew Bostick <andrew.bostick1.gmail.com>
wrote:
> 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 - 01:30:03 PDT
