[gmx-users] (no subject)

[Nguyen Hoang Phuong]

>
> 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?
you can use the program trjconv:

trjconv -f x.trr -s x.tpr -o x.gro -n index.ndx


where the file index.ndx look like

[atom]
3
4
5
6

the ouput file is x.gro

Phuong


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