All the mdcrd file is is a set of coordinates. One thing you'll have
to remember is that the first line is a title line (blank if no title)
and the second line is the number of atoms. Thus, open a blank file,
copy the first two lines from the original mdcrd to the new file, and
then go to the end of any frame (including the box information if
you're using PBC), but probably one toward the middle. You can
probably calculate the number of lines you'll have to scroll down by
recognizing there are 3 coordinates per atom and 10 coordinates per
line, with an additional line for box information.
Then delete from that line to the end of the file and paste it into
the new one. However, if these files are too large to manipulate with
ptraj, these operations could take some time.
As a side note, did you compile ptraj with large file support? Is it
compiled that way by default? I would not really know this, but
someone else may know if a ptraj compiled with LFS does still have a
size limit short of a couple terabytes on a 64-bit system...
Good luck!
Jason
On Wed, Mar 17, 2010 at 11:54 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> I did an MD simulation and had my ntwx parameter set too small. As a
> result, the *.mdcrd file is very large, and ptraj will not open it. Is
> there a way to split the *.mdcrd file into two equal but smaller files?
>
>
>
> John
>
>
>
>
>
>
>
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>
>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Mar 17 2010 - 09:30:03 PDT
