[gmx-users] g_covar for many large runs

David spoel at xray.bmc.uu.se
Tue Apr 5 21:44:47 CEST 2005

On Tue, 2005-04-05 at 11:53 -0700, Sichun Yang wrote:
> Hi,
> I have generated around 1,000 large runs, and each run has about 1GB
> output. How can I avoid using trjcat to generate one 'HUGE' file in order
> to get g_covar done?
That would be a 1 Tb file. Interesting.

You'll have to modify g_covar such that it can read multiple files
sequentially and process them. Check trjcat for the multi-file reading
code. I'm afraid it will take a long time. An alternative would be to
modify g_covar to write out the covariance matrix before diagonalizing,
then write a program to read all the 1000 covariance matrices and sum

It would be very nice if reading many files could be done automatically
because it would make the whole trjcat business superfluous... All the
logic is there, it just has to be combined into a library function.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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