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

[Nuno Ricardo Loureiro Ferreira]

Yuhua Song <yhsong at ccb.wustl.edu> escreveu:

> Hi,
> Thanks, I check the mailing-list. and I find the information as below:
> 
> "break down the big file into smaller pieces using 'split'.
> You have to know the number of frames, the filesize and then
> divide the filesize by frames+1. This will give you the
> size per frame. And then you can make the chunks you want...."
> 
> my file cases is: 7ns: 3500frames. 

I think it has 3501 frames.
Check with gmxcheck -f *.trr


>one frame size is 1410block, If I want to
> split the *.trr file in 1ns chunks ( 1ns has 500 frames),  the split size
> should be (500*oneframesize) or (501*oneframesize)?. I am a little confused
> how to deal with that extra one frames, the extra one frame is at the
> beginning of the file or at the end of the file?
> 

This extra frame comes from time=0. So, if you have 7 ns run with an 
nstxout=1000 and a dt=0.002 (or something like that), you will have 3500 
frames (snapshots at t=2,4,6...,70000ps) plus the snapshot at t=0.

After having the size per frame, to cut your 7ns traj. in 500 frame pieces as 
you asked, cut the traj into 1 piece of 501 and 6 pieces of 500 frames.
It's more clear now?

NUno