What is the *.trj file? Are you talking about the trajectory file, mdcrd?
If so, all you'll get from that are the system conformations at different
timesteps. The combination of grep/awk is quite useful for extracting this
kind of information, as are python/perl scripts as Bill suggested. I've
attached a Python script I wrote that will extract all of this information
and write gnuplot scripts so that you can visualize it easily. You need
Python-2.6 to run the script, though. You can get the script at
qtp.ufl.edu/~swails/Files/analyzeConvergence.py . It may be helpful to
learn how to do this on your own, though, as python/perl can be very useful
tools.
Good luck!
Jason
On Mon, Aug 2, 2010 at 2:06 AM, setyanto tri wahyudi <stwahyudi.gmail.com>wrote:
> dear Ross,
>
> Thank you for suggestion. Should I extract the information from mdout using
> *.trj file ?
> thanks.
>
> On Mon, Aug 2, 2010 at 12:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > This could be a good time to learn awk or perl, to write simple
> > programs to process text files. You may also want to look at the
> > mden file - I forget the format but believe it is easier to parse
> > than mdout.
> >
> > Bill
> >
> > _______________________________________________
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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 Mon Aug 02 2010 - 05:30:09 PDT
