[gmx-users] g_covar for many large runs

[T.A.Wassenaar]

Hi,

Actually, g_covar writes out the covariance matrix in xpm 
format with the option -xpm. You would have to get/write a 
script that is able to average these .xpm files. 'convert' 
from the ImageMagick suite can do this. You can output the 
average again to xpm (I think) or use an image format such 
as ppm. Then you'd have to diagonalize the resulting 
matrix to obtain the eigenvectors and -values. For this 
you could use matlab, though I don't know whether it can 
read .ppm or other image formats.

Hope it helps,

Tsjerk

On Tue, 5 Apr 2005 12:59:10 -0700 (PDT)
  Sichun Yang <syang at physics.ucsd.edu> wrote:
> 
> Just curious, how long would it take to generate this 
>1TB file if I tried?
> 
> -Sichun
> 
> On Tue, 5 Apr 2005, David wrote:
> 
>> 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
>> them.
>> 
>> 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.
>> ________________________________________________________________________
>> 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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