Hi Dan,
This does seem like it would fix the issue and get what I need.
However, now I'm running into an error with the 'runanalysis' command. This
is the error generated by the output:
[runanalysis avg oversets BB? out Avg.dat]
Warning: 'oversets' selects no data sets.
Warning: 'BB?' selects no data sets.
Error: No data sets selected.
Error: Could not add data sets.
I'm using cpptraj v.14.01, so I'm not sure if it's completely up to date
with the syntax. Any suggestions?
Thanks for your assistance,
Hunter
On Mon, Jan 14, 2019 at 6:42 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This can be done; you just need to process each trajectory separately.
> For example:
>
> parm 2fct_WT_solv.prmtop
> reference ../2fct_WT_npt2.rst
> # Traj 1
> trajin ../1/2fct_WT_nvt-binary.nc
> autoimage
> rmsd BB1 :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
> run
> clear trajin
> # Traj 2
> trajin ../2/2fct_WT_nvt-binary.nc
> autoimage
> rmsd BB2 :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
> run
> clear trajin
> # Traj 3
> trajin ../1/2fct_WT_nvt-binary.nc
> autoimage
> rmsd BB3 :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
> run
> clear trajin
> # Average
> runanalysis avg oversets BB? out Avg.dat
>
> If you have a recent (i.e. AmberTools 18 or GitHub) version of
> cpptraj, you can use a for loop to simplify things:
>
> parm 2fct_WT_solv.prmtop
> reference ../2fct_WT_npt2.rst
> for i=1;i<4;i++
> trajin ../$i/2fct_WT_nvt-binary.nc
> autoimage
> rmsd BB$i :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
> run
> clear trajin
> done
> runanalysis avg oversets BB? out Avg.dat
>
> Hope this helps,
>
> -Dan
>
> On Mon, Jan 14, 2019 at 4:25 PM Hunter Wilson <wils1872.umn.edu> wrote:
> >
> > Afternoon all,
> >
> > I want to calculate an average RMSD across the timescale of my simulation
> > by using three independent trajectories as inputs. Currently, cpptraj is
> > catenating all of the three trajectories when calculating the RMSD. Below
> > is my input script:
> >
> > trajin ../1/2fct_WT_nvt-binary.nc
> > trajin ../2/2fct_WT_nvt-binary.nc
> > trajin ../3/2fct_WT_nvt-binary.nc
> > reference ../2fct_WT_npt2.rst
> > center :1-308
> > image
> > rmsd BB :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
> >
> > And this is the output:
> > PARAMETER FILES:
> > 0: '2fct_WT_solv.prmtop', 39040 atoms, 11749 res, box: Orthogonal, 11443
> > mol, 11408 solvent, 18750 frames
> >
> > INPUT TRAJECTORIES:
> > 0: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
> > 2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
> > 1: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
> > 2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
> > 2: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
> > 2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
> > Coordinate processing will occur on 18750 frames.
> >
> > REFERENCE FRAMES (1 total):
> > 0: '../2fct_WT_npt2.rst', frame 1
> > Active reference frame for masks is 0
> > TIME: Run Initialization took 0.0001 seconds.
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM '2fct_WT_solv.prmtop' (3 actions):
> > 0: [center :1-308]
> > Mask [:1-308] corresponds to 4783 atoms.
> > 1: [image]
> > Number of molecules to be imaged is 11443 based on mask '*'
> > 2: [rmsd BB :110.C,CA,N,:229.C,CA,N,:305-308 first mass out
> rmsd-BB.dat]
> > Mask [:110.C,CA,N,:229.C,CA,N,:305-308] corresponds to 21 atoms.
> > Mask [:110.C,CA,N,:229.C,CA,N,:305-308] corresponds to 21 atoms.
> > 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.
> > ----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
> > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > ----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
> > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > ----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
> > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> >
> > Read 18750 frames and processed 18750 frames.
> > TIME: Trajectory processing: 32.2032 s
> > TIME: Avg. throughput= 582.2396 frames / second.
> >
> > ACTION OUTPUT:
> >
> > DATASETS:
> > 1 data set:
> > BB "BB" (double, rms), size is 18750
> >
> > DATAFILES:
> > rmsd-BB.dat (Standard Data File): BB
> > ---------- RUN END ---------------------------------------------------
> > TIME: Total execution time: 32.6381 seconds.
> >
> --------------------------------------------------------------------------------
> > ,
> > The output gives the RMSD of my mask over 18750 frames, when what I want
> is
> > the average value of the three simulations, which will only give 6250
> > frames. Any tips or suggestions?
> >
> > Best,
> > Hunter
> > --
> > Hunter Wilson
> > Chemistry PhD Student
> > General Chemistry Teaching Assistant
> > wils1872.umn.edu
> >
> > Department of Chemistry
> > University of Minnesota- Twin Cities
> > _______________________________________________
> > 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
>
--
Hunter Wilson
Chemistry PhD Student
General Chemistry Teaching Assistant
wils1872.umn.edu
Department of Chemistry
University of Minnesota- Twin Cities
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Received on Tue Jan 15 2019 - 06:00:02 PST
