Hello,
netcdf is a binary array-storing format, which perfectly suits our
needs of storing an array of coordinates for a trajectory. Check out
the ioutfm input variable for sander and pmemd (which belongs in the
&cntrl namelist), which specifies the output of trajectories in
netcdf. In order to use this, however, you need to have installed
sander with binary trajectory support (I believe it is by default).
Same with pmemd (which is not done by default). If you are compiling
amber yourself, then use the configure script for pmemd in its regular
form, but add "pubfft bintraj" at the end.
To transform a trajectory from ASCII to netcdf, use ptraj (where you
must follow a netcdf file with "netcdf" to specify that format). This
is all detailed in the manual as well.
Good luck!
Jason
2010/3/16 Nancy <song_jianing_hi.126.com>:
> Dear all,
> I'm writing to ask you if you'd like to give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER.
> My resent research needs to calculate a 10ns trajectory , and it will be too large if the trajectory is in ASCII formate, so I want to get a binary one.
> I search AMBER10 user guide. It says that NetCDF can help to do this, but actually I don't know how to ,you konw , I'm just a new AMBER user.
> I would really appreciate it if you'd like to give me some advice.
> Thank you very much!
> Sincerely yours,
> Jianing Song
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 16 2010 - 19:30:02 PDT
