IMO binpos is not agreat file format for this. It's better to convert to
DCD file.
Hai
On Mon, Sep 26, 2016 at 9:25 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
> Hi Bostick,
>
> As Jason told there is no netcdf in windows, I guess you are using VMD in
> windows. Please change your trajectory in binpos, windows version of VMD
> accepts it. However you may face issue in loading trajectories if it is
> large. Windows version of VMD is not good for big trajectories. You may use
> following cpptraj input to get binpos trajectory and then load in VMD.
>
> parm prmtop-file
> trajin trajin-file.nc netcdf
> autoimage
> trajout filename.binpos binpos
>
> Hope it will help.
>
> Kshatresh
>
> On Sun, Sep 25, 2016 at 7:58 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With best regards
> ************************************************************
> ************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 26 2016 - 11:00:03 PDT
