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
> >
> >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 21 2021 - 05:30:13 PST
