Thanks for the reply. I have tried cpptraj following your suggestion but I
am unable to unwrap the trajectory using cpptraj. I have no prior
experience of using cpptraj. Also asterisks are not observed in the
original ASCII trajectory file. As I have mentioned earlier, I have used
iwrap=1 during my production run.
On Tue, Apr 14, 2015 at 7:36 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Apr 13, 2015 at 10:42 PM, pooja chahal
> <chahal.pooja.rs.gmail.com> wrote:
> > Also one more thing that I am observing is that while generating .pdb
> files
> > using ptraj with unwrap command, some of atoms attains a very high
> negative
> > value (< -1000) for coordinates. For these coordinates "********" appears
> > in the .pdb file instead of real coordinates. However, this is not the
> only
>
> This seems odd to me. The multiple asterisks is something that fortran
> code does for numerical overflow, not C/C++ code (to my knowledge).
> You shouldn't be getting asterisks in your PDB files if you're
> creating them with ptraj. Do you get the same behavior with cpptraj?
>
> If on the other hand you mean you see asterisks in the original ASCII
> trajectory file then your coordinates overflowed during your
> simulation and there is no way to recover them. For this reason it is
> recommended that during simulations you use 'iwrap=1' to enable
> imaging, 'ioutfm=1' to write NetCDF trajectories, and 'ntxo=2' to
> write NetCDF restart files; the NetCDF file format is not nearly as
> susceptible to issues as the ASCII format.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> 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 Wed Apr 15 2015 - 05:30:02 PDT
