Dear Gustaf and Daniel,
Yes, I had not, somehow, paid attention to the periodic box boundary while
loading.
Thank you for the help.
--Chetna
On Thu, May 3, 2018 at 4:32 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The image you attached looks like you may have a mismatch between your
> topology and trajectory file. Make sure you're using the same topology
> that was used to generate the trajectory. Also, if your ASCII
> trajectory has box coordinates make sure you select "Amber coordinates
> with periodic box" - VMD will not detect this automatically.
>
> -Dan
>
> On Thu, May 3, 2018 at 10:18 AM, 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best wishes
Chetna
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Received on Thu May 03 2018 - 08:00:04 PDT
