If you are running VMD on a Windows machine, NetCDF files won't work. It's
not that NetCDF won't build on Windows (I've cross-compiled a NetCDF dll on
Linux that worked just fine on Windows recently). But it's not something
that the VMD developers have put a priority on (and we are not associated
with VMD development).
So at the end of the day, if you need to use Windows, you will need to use
cpptraj to convert to DCD or some other format supported on the platform.
VMD on Mac and Linux both support NetCDF trajectories.
HTH,
Jason
On Sun, Sep 25, 2016 at 4:20 AM, Andrew Bostick <andrew.bostick1.gmail.com>
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
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 25 2016 - 10:00:04 PDT
