Hi,
First, the input you posted doesn't correspond to the output. Here's
the rms command from your input:
On Wed, Mar 16, 2016 at 1:04 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> rms first out rmsd-zinctes.dat .C,CA,N time 10.0
Here is the rms command in your output:
> 4: [rms first out rmsd-zinctes.dat .C,CA,N time 2.0]
Here you are setting the 'time' argument to 2.0, so cpptraj multiplies
each frame you have by '2'. Since you have 30000 frames, the final X
value is 60000.
-Dan
> Target mask: [.C,CA,N](791)
> Reference mask: [.C,CA,N](791)
> Warning: Coordinates are being rotated and box coordinates are present.
> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> Warning: after the RMS-fit is performed.
> ----- itk1.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk2.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk3.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk4.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk5.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk6.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk7.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk8.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk9.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk10.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk11.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk12.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk13.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk14.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk15.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk16.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk17.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk18.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk19.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk20.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk21.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk22.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk23.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk24.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk25.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk26.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk27.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk28.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk29.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- itk30.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 30000 frames and processed 30000 frames.
> TIME: Trajectory processing: 723.6999 s
> TIME: Avg. throughput= 41.4536 frames / second.
>
> ACTION OUTPUT:
>
> DATASETS:
> 1 data set:
> RMSD_00000 "RMSD_00000" (double, rms), size is 30000
>
> DATAFILES:
> rmsd-zinctes.dat (Standard Data File): RMSD_00000
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 724.7298 seconds.
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
> Thank you.
> Best Regards, Saman Yousuf Ali
>
>
> On Wednesday, March 16, 2016 4:58 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
>
> On Wed, 16 Mar 2016 11:47:52 +0000
> Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>
>> trajin md_simulation_combine.nc
>> rms first :1-532.CA,C,N out rmsd.dat
>> strip :WATER
>> strip :Na+
>
> You are reading a single trajectory file here. How many frames does it
> contain, how have you created this file? Check this first.
>
> As far as cpptraj is concerned there is no need to combine trajectories
> beforehand. I would recommend to use multiple "trajin" commands to
> read in the original files.
>
> The rms command has an option "time" which you can use to scale the
> x-axis to your liking. See the manual. If you do not use "time" then
> the x-axis is simply the number of frames. So why does the file
> md_simulation_combine.nc have so many? You originally indicated there
> should be only half that number.
>
> The final "strip" commands don't seem to do anything useful here (unless
> your script is longer and you do something else with the stripped
> topology later). I suspect that the ":WATER" mask should actually
> be ":WAT".
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 16 2016 - 12:30:05 PDT
