My version is 1.9.2 on OSX, and it has a NetCDF option (alphabetically
listed).
Bill
On 9/25/16 1:20 AM, Andrew Bostick wrote:
> 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 - 10:00:02 PDT
