[gmx-users] Re: rerun of trajectory

[Anton Feenstra]

Swetha Vijayakrishan wrote:
> hi,
> 
> actually the trr file is about 5.3G.its really huge as i have
> saved the velocities every 0.2ps.also i ran the tpbconv command from the
> same dir which has the .trr file.But it still does not seem to recognize
> it.

Reading files >2Gb often gives problems. We've had it here also. Although
'large file support' was enabled in the OS and on Gromacs, all tools
refused to recognize the file. The solution, in our case, was to calculate
the size of each frames (is filesize/nframes, beware that mdrun always
writes the last frame of the simulation, so you often have one more than
you expect). Then, you can use the UNIX command 'split' to split the file
into portions (e.g. 3 parts of <2Gb each) with whole frames. Convert these
separate .trr files to .xtc, or remove water, and then recombine or analyze
them separately.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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