Thank you for your reply. I will follow your suggestions and get back if
the problem is not solved.
-harsh
On Tue, Oct 21, 2014 at 5:09 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, 2014-10-21 at 13:26 +0530, Harshavardhan Khare wrote:
> > Dear all,
> >
> > I am trying to simulate a protein with 6 chains. Everything goes fine up
> to
> > 1 ns. From approximately 1.5 ns onwards, 3 chains are missing from the
> > coordinates.
>
> What do you mean when you say 3 chains are "missing"? Their coordinates
> are NaN? Inf? Do they move to the other side of the box (appearing to
> "disassociate" from the other chains)?
>
> The number of atoms in sander and pmemd _never_ changes, and all
> coordinates are _always_ printed out for every frame. The literal
> definition of what you said (i.e., that sander or pmemd suddenly stopped
> printing out the coordinates for 3 chains such that their coordinates
> simply don't exist) seems impossible. For one thing, this would corrupt
> the NetCDF trajectory file and cause any programs reading them (like
> VMD) to spit out an error and show nothing at all.
>
> You can use the "ncdump" program to look at the actual data stored in a
> NetCDF file. That might help you determine whether some of the
> coordinates went off to NaNdyland.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Oct 22 2014 - 04:30:02 PDT
