[gmx-users] Problems with trjconv, file too big

Nuno Ricardo Loureiro Ferreira nunolf at ci.uc.pt
Tue Dec 30 02:12:00 CET 2003

Hi Yuhua Song 

> Thanks, Nuno,
> > I think it has 3501 frames.
> > Check with gmxcheck -f *.trr
> Becuase the file is too big, so gmxcheck does not work also.

Sorry, I forgot that.

> > After having the size per frame, to cut your 7ns traj. in 500 frame 
> as
> > you asked, cut the traj into 1 piece of 501 and 6 pieces of 500 frames.
> > It's more clear now?
> Thanks, I understand this. but when I split the big *.trr file using:
> split -b size of 501frame -b size of 500frame*6  *.trr
> it does not work, it seems that split can only split the big file into the
> small chunk of same size,

Yes, you are right. 

 what is your way to split the big file into small
> chunks? Please do not tell me that split the big file into 3501 files, then
> combine them together. I thinks that there should have some ways to split
> into several limited files such as 2ns interval, 1ns interval etc.

Your main concern is to split your big trr file into smaller ones in a way 
you can analyse under gmx, isn't it?
So, split it into some chunks, does not matter the number of frames in each 
one. The only rule is to be smaller then 2GB.
Then, if you are not interested in the solvent and ions, save from each 
chunk only the protein stuff (in xtc). After that, join the protein chunks 
and analyse it.


P.S. When I have big trajs, I usually split them into pieces that fit in the 
CD. If you have a DVD, then saving the work is not a problem for you.

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