Hi, sorry for the delay in replying.
So the "coords 1 & 2 overlap at origin" message means exactly that;
the coordinates for atoms 1 and 2 are both at the origin, i.e. they
are both 0,0,0. I put this in as a quick-and-dirty check for bad input
coordinates, since in my experience this is usually how write failures
manifest themselves (at least with binary trajectory formats). This
can happen for a lot of reasons, but it's almost always a filesystem
issue. Either the device temporarily ran out of space, there was a
hiccup in the NFS mount, etc etc. It looks like all of the warnings
are triggered by the "339t29_md7.nc" trajectory, so something happened
during that simulation. If you ran on a cluster you can ask the
systems admins to check logs to see if something was going on with the
network or filesystem during that time.
Unfortunately there is no recovering the bad frames. Using
'skipbadframes' the way that you are is the best way to get around it.
Hope this clarifies things,
-Dan
On Sun, Feb 21, 2021 at 11:32 AM Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
>
> yes this does suggest that the 339t29_md7.nc file has been corrupted,
> perhaps it is a filesystem issue. Dan Roe may have more suggestions on what
> cpptraj is encountering.
>
> On Sun, Feb 21, 2021 at 9:13 AM Victoria E Hill <vehill1.sheffield.ac.uk>
> wrote:
>
> > I used the following input file for cpptraj:
> > parm 339t29.parm7
> > trajin 339t29_md4.nc
> > trajin 339t29_md5.nc
> > trajin 339t29_md6.nc
> > trajin 339t29_md7.nc
> > trajout 339t29_fixed_md4_5_6_7.crd
> > go
> > quit
> >
> > Which gave the following output:
> > CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.11)
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 02/21/21 14:08:11
> > | Available memory: 7.300 GB
> >
> > INPUT: Reading input from 'cpptraj.in'
> > [parm 339t29.parm7]
> > Reading '339t29.parm7' as Amber Topology
> > Radius Set: ArgH and AspGluO modified Bondi2 radii (mbondi3)
> > [trajin 339t29_md4.nc]
> > Reading '339t29_md4.nc' as Amber NetCDF
> > [trajin 339t29_md5.nc]
> > Reading '339t29_md5.nc' as Amber NetCDF
> > [trajin 339t29_md6.nc]
> > Reading '339t29_md6.nc' as Amber NetCDF
> > [trajin 339t29_md7.nc]
> > Reading '339t29_md7.nc' as Amber NetCDF
> > [trajout 339t29_fixed_md4_5_6_7.crd]
> > Writing '339t29_fixed_md4_5_6_7.crd' as Amber Trajectory
> > [go]
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: 339t29.parm7, 21564 atoms, 678 res, box: None, 2 mol
> >
> > INPUT TRAJECTORIES (4 total):
> > 0: '339t29_md4.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 1: '339t29_md5.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 2: '339t29_md6.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 3: '339t29_md7.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > Coordinate processing will occur on 4000 frames.
> >
> > OUTPUT TRAJECTORIES (1 total):
> > '339t29_fixed_md4_5_6_7.crd' (4000 frames) is an AMBER trajectory
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTIVE OUTPUT TRAJECTORIES (1):
> > 339t29_fixed_md4_5_6_7.crd (coordinates, time)
> > ----- 339t29_md4.nc (1-1000, 1) -----
> > 0% 10% 20%
> > ----- 339t29_md5.nc (1-1000, 1) -----
> > 30% 40%
> > ----- 339t29_md6.nc (1-1000, 1) -----
> > 50% 60% 70%
> > ----- 339t29_md7.nc (1-1000, 1) -----
> > Warning: Frame 69 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 96 coords 1 & 2 overlap at origin; may be corrupt.
> > 80% Warning: Frame 276 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 308 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 477 coords 1 & 2 overlap at origin; may be corrupt.
> > 90% Warning: Frame 880 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 961 coords 1 & 2 overlap at origin; may be corrupt.
> > 100% Complete.
> >
> > Read 4000 frames and processed 4000 frames.
> > TIME: Avg. throughput= 48.3770 frames / second.
> >
> > ACTION OUTPUT:
> > TIME: Analyses took 0.0000 seconds.
> >
> > RUN TIMING:
> > TIME: Init : 0.0026 s ( 0.00%)
> > TIME: Trajectory Process : 82.6839 s ( 99.92%)
> > TIME: Action Post : 0.0000 s ( 0.00%)
> > TIME: Analysis : 0.0000 s ( 0.00%)
> > TIME: Data File Write : 0.0000 s ( 0.00%)
> > TIME: Other : 0.0602 s ( 0.00%)
> > TIME: Run Total 82.7467 s
> > ---------- RUN END ---------------------------------------------------
> > [quit]
> > TIME: Total execution time: 82.8134 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.
> > CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.11)
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 02/21/21 14:08:11
> > | Available memory: 7.300 GB
> >
> > INPUT: Reading input from 'cpptraj.in'
> > [parm 339t29.parm7]
> > Reading '339t29.parm7' as Amber Topology
> > Radius Set: ArgH and AspGluO modified Bondi2 radii (mbondi3)
> > [trajin 339t29_md4.nc]
> > Reading '339t29_md4.nc' as Amber NetCDF
> > [trajin 339t29_md5.nc]
> > Reading '339t29_md5.nc' as Amber NetCDF
> > [trajin 339t29_md6.nc]
> > Reading '339t29_md6.nc' as Amber NetCDF
> > [trajin 339t29_md7.nc]
> > Reading '339t29_md7.nc' as Amber NetCDF
> > [trajout 339t29_fixed_md4_5_6_7.crd]
> > Writing '339t29_fixed_md4_5_6_7.crd' as Amber Trajectory
> > [go]
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: 339t29.parm7, 21564 atoms, 678 res, box: None, 2 mol
> >
> > INPUT TRAJECTORIES (4 total):
> > 0: '339t29_md4.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 1: '339t29_md5.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 2: '339t29_md6.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > 3: '339t29_md7.nc' is a NetCDF AMBER trajectory with coordinates, time,
> > Parm 339t29.parm7 (reading 1000 of 1000)
> > Coordinate processing will occur on 4000 frames.
> >
> > OUTPUT TRAJECTORIES (1 total):
> > '339t29_fixed_md4_5_6_7.crd' (4000 frames) is an AMBER trajectory
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTIVE OUTPUT TRAJECTORIES (1):
> > 339t29_fixed_md4_5_6_7.crd (coordinates, time)
> > ----- 339t29_md4.nc (1-1000, 1) -----
> > 0% 10% 20%
> > ----- 339t29_md5.nc (1-1000, 1) -----
> > 30% 40%
> > ----- 339t29_md6.nc (1-1000, 1) -----
> > 50% 60% 70%
> > ----- 339t29_md7.nc (1-1000, 1) -----
> > Warning: Frame 69 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 96 coords 1 & 2 overlap at origin; may be corrupt.
> > 80% Warning: Frame 276 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 308 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 477 coords 1 & 2 overlap at origin; may be corrupt.
> > 90% Warning: Frame 880 coords 1 & 2 overlap at origin; may be corrupt.
> > Warning: Frame 961 coords 1 & 2 overlap at origin; may be corrupt.
> > 100% Complete.
> >
> > Read 4000 frames and processed 4000 frames.
> > TIME: Avg. throughput= 48.3770 frames / second.
> >
> > ACTION OUTPUT:
> > TIME: Analyses took 0.0000 seconds.
> >
> > RUN TIMING:
> > TIME: Init : 0.0026 s ( 0.00%)
> > TIME: Trajectory Process : 82.6839 s ( 99.92%)
> > TIME: Action Post : 0.0000 s ( 0.00%)
> > TIME: Analysis : 0.0000 s ( 0.00%)
> > TIME: Data File Write : 0.0000 s ( 0.00%)
> > TIME: Other : 0.0602 s ( 0.00%)
> > TIME: Run Total 82.7467 s
> > ---------- RUN END ---------------------------------------------------
> > [quit]
> > TIME: Total execution time: 82.8134 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.
> >
> > Then using 'check skipbadframes silent'' in the input file solves the
> > problem.
> >
> > Victoria
> >
> >
> > On Sun, 21 Feb 2021 at 13:56, Carlos Simmerling <
> > carlos.simmerling.gmail.com>
> > wrote:
> >
> > > please include the cpptraj output so we can see what you did and what
> > > messages it gives
> > >
> > > On Sun, Feb 21, 2021 at 8:36 AM Victoria E Hill <vehill1.sheffield.ac.uk
> > >
> > > wrote:
> > >
> > > > Yes, I used cpptraj and that gave me the warnings.
> > > >
> > > > Victoria
> > > >
> > > > > On 21 Feb 2021, at 13:27, Carlos Simmerling <
> > > carlos.simmerling.gmail.com>
> > > > wrote:
> > > > >
> > > > > how did you convert to crd, with cpptraj? which program gave you
> > those
> > > > > warnings?
> > > > >
> > > > >> On Sun, Feb 21, 2021 at 7:58 AM Victoria E Hill <
> > > > vehill1.sheffield.ac.uk>
> > > > >> wrote:
> > > > >>
> > > > >> Thank-you for your reply.
> > > > >>
> > > > >> I ran my simulations as .nc files but had to change them to .crd in
> > > > order
> > > > >> to visualise them with VMD (I’m on a windows computer) and got the
> > > > ‘atoms
> > > > >> overlapping at origin’ warnings which I saw online were due to
> > > > corruption.
> > > > >> Is this not the case?
> > > > >>
> > > > >> Even so, why are netcdf less prone to corruption?
> > > > >>
> > > > >> Thanks,
> > > > >> Victoria
> > > > >>
> > > > >>>> On 21 Feb 2021, at 10:57, Maria Nagan <maria.c.nagan.gmail.com>
> > > > wrote:
> > > > >>>
> > > > >>> Are you sure they’re corrupted and not just netcdf trajectories?
> > > > >> Sometimes with the mdcrd text files I’ve had corruption but not on
> > > only
> > > > 10
> > > > >> ns. Also sometimes the transfer process affects this. Make sure
> > you’re
> > > > >> using netcdf files. They are less prone to corruption.
> > > > >>>
> > > > >>>> On Feb 20, 2021, at 11:36 AM, Victoria E Hill <
> > > > vehill1.sheffield.ac.uk>
> > > > >> wrote:
> > > > >>>>
> > > > >>>> Hi,
> > > > >>>>
> > > > >>>> I have been running some 10 ns simulations and almost all are
> > > > >> corrupted. I
> > > > >>>> know how to fix this with 'skipbadframes' but I was wondering why
> > > this
> > > > >>>> happens? As I wasn't able to find an explanation online.
> > > > >>>>
> > > > >>>> Thanks,
> > > > >>>> Victoria
> > > > >>>>
> > > > >>>> --
> > > > >>>> *Victoria Hill*
> > > > >>>>
> > > > >>>> PhD student, Craggs lab
> > > > >>>> Department of Chemistry
> > > > >>>> University of Sheffield
> > > > >>>> _______________________________________________
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Received on Tue Feb 23 2021 - 11:30:02 PST
