The 'binpos' format doesn't store unit cell information. If your
trajectory doesn't have box info then binpos is probably fine.
-Dan
On Fri, Sep 30, 2016 at 4:29 AM, Karolina Mitusińska (Markowska)
<markowska.kar.gmail.com> wrote:
> Hi there,
>
> I'd like to bring this topic up and ask: why is binpos not a great file to
> convert .nc files to? And why is DCD better? What's the difference?
>
> Looking forward to any explanations :)
>
> Have a nice day!
> Karolina
> PhD student
>
>
> 2016-09-26 19:31 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
>
>> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 30 2016 - 05:30:05 PDT
