Dear Daniel
It is showing 2185 frames. However, I have checked and rechecked. The .out
file shows the completion of 50lakhs steps. It did not get terminated;
neither is the trajectory showing any artifacts.
I have faced a similar situation earlier, wherein each time I was loading
the frames in VMD, each time the frame number was increasing! I am very
confused.
Thanks
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*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
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On Tue, Aug 25, 2015 at 8:04 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If this is a netcdf trajectory you can see exactly how many frames are
> in it without even going through cpptraj or vmd using the ncdump
> command with '-h', e.g. "ncdump -h mytraj.nc". Right near the top
> you'll see something like:
>
> frame = UNLIMITED ; // (X currently)
>
> If X is 2000 then there are indeed only 2000 frames in the trajectory.
> This probably means one of 2 things:
>
> 1) The run terminated before nstlim was reached after only 2000 frames
> were written.
>
> 2) You're comparing the trajectory to the wrong output file and
> actually had nstlim set to 2000000 for the run.
>
> It's hard for me to come up with any other scenarios based on the
> given information. Is the trajectory otherwise OK? When you visualize
> it are there any artifacts?
>
> -Dan
>
>
> On Tue, Aug 25, 2015 at 8:22 AM, MOHD HOMAIDUR RAHMAN
> <rahmanhpu.gmail.com> wrote:
> > On Tue, Aug 25, 2015 at 5:50 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> here is probably not much you can do: since this is a netcf
> >
> >
> > Thank you Prof. Case
> >
> > The cpptraj load trajectory without any error message.
> >
> > Regards
> > Rahman
> >
> >
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Tue Aug 25 2015 - 11:30:03 PDT
