Dear Loeffler,Thank you so much for your guidance and kind cooperation. I have also run cpptraj rmsd command using multiple trajin, as you recommended me. I got same valueon x-axis, 60000 frames. Kindly tell me the rms command, which has an option "time" to scale the x-axis or tell me link of manual. Input file and command are pasted below,input:
trajin itk1.mdcrd
trajin itk12.mdcrd
trajin itk13.mdcrd
trajin itk14.mdcrd
trajin itk15.mdcrd
trajin itk16.mdcrd
trajin itk17.mdcrd
trajin itk18.mdcrd
trajin itk19.mdcrd
trajin itk20.mdcrd
trajin itk21.mdcrd
trajin itk22.mdcrd
trajin itk23.mdcrd
trajin itk24.mdcrd
trajin itk25.mdcrd
trajin itk26.mdcrd
trajin itk27.mdcrd
trajin itk28.mdcrd
trajin itk29.mdcrd
trajin itk30.mdcrd
center :1-263
image familiar
strip :WAT
strip :NA+
rms first out rmsd-zinctes.dat @C,CA,N time 10.0
command:cpptraj -p itk.prmtop -i rmsd.in
output:BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'itk.prmtop' (5 actions):
0: [center :1-263]
Mask [:1-263] corresponds to 4177 atoms.
1: [image familiar]
Number of molecules to be imaged is 9514 based on mask '*'
2: [strip :WAT]
Stripping 28506 atoms.
Stripped parm: 'itk.prmtop', 4230 atoms, 274 res, box: Orthogonal, 12 mo
l
3: [strip :NA+]
Stripping 0 atoms.
Warning: No atoms to strip. Skipping 'strip' for topology 'itk.prmtop'
Warning: Setup failed for [strip :NA+]: Skipping
4: [rms first out rmsd-zinctes.dat @C,CA,N time 2.0]
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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Received on Wed Mar 16 2016 - 12:30:04 PDT
