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 Sun Feb 21 2021 - 06:00:04 PST
