[gmx-users] (no subject)

[Andreas Kukol]

>>> herbst at fhi-berlin.mpg.de 05/10/2004 11:16:24 >>>
Hi all,

I need to read the coordinates of certain atoms from my trr-file from my
simulation. I have seen that the trr file can be converted to ascii with
gmxdump, but the files are very large,and for I have 500 ns simulations
and I need to do that for a lot of simulations, I do not have enough
space.
Is there any way to extract only the coordinates for, say, atom 3 - 6, for
every timestep? How would you do it?

Thanks,
Anna

This should be possible with TRJCONV, this program has an interactive dialogue, where you can choose which part of the system (protein, backbone, etc) should be written to your new trajectory. If the standard choices are not enough, you need to supply an index file, which contains the atoms you want.
The index file is made with MAKE_NDX

Regards
Andreas