It looks like you have an issue with correction for molecules jumping the periodic border. Did you use periodic boundary conditions and in that case did you open as …. with periodic box.
// Gustaf
> On 3 May 2018, at 16:18, Chetna Tyagi <cheta231.gmail.com> wrote:
>
> Dear all,
>
> I prepared prmtop and inpcrd files using Ambertools16 or 18 and ran the
> initial minimization, equilibration using sander but for the production run
> I used the university's pmemd.cuda engine of Amber14. The university server
> has only Amber14 version.
>
> When I try to load the resultant netcdf files .nc in VMD it shows "Could
> not open file" error and when I change it to .mdcrd format, it loads and
> looks something like this.
>
>
>
>
> The calculation runs without error reports and using the same input files
> and parameters on my AmberTools sander.MPI, no such errors occur.
>
> Please advice if I can correct these production.nc files as re-doing these
> simulations on my desktop computer will cost me a lot.
>
> --
> Best wishes
> Chetna
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Received on Thu May 03 2018 - 07:30:06 PDT
