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
> > > >>>> _______________________________________________
> > > >>>> AMBER mailing list
> > > >>>> AMBER.ambermd.org
> > > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>>
> > > >>>
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Received on Sun Feb 21 2021 - 09:00:03 PST
