[gmx-users] trjconv for cutting the trajectory in small subtrajectories

[Mahboobeh Eslami]

Thanks my friendsI checked new trajectory by gmxcheck and get following text:
Reading frame       0 time 7000.000   
# Atoms  8383
Precision 0.001 (nm)
Reading frame    5000 time 17000.000   
Item        #frames Timestep (ps)
Step          5501    2
Time          5501    2
Lambda           0
Coords        5501    2
Velocities       0
Forces           0
Box           5501    2
Reading frame is 5000 but desired frames are 5500 frame. I'm confused.best
 


     On Saturday, April 25, 2015 5:42 PM, James Lord <jjamesgreen110 at gmail.com> wrote:
   

 Hi Mahboobeh,I recommend checking the created trajectories with gmx check. CheersJames
On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

Hi，-e is end frame， -b is the start one.

Sent from my Huawei Mobile

Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:

hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the  trajectory  in  small   subtrajectories from 10000ps to 17000ps by following command:
trjconv -f md.xtc -s md.tpr -n index.ndx -e 10000 -b 17000
I see following text in terminal window;
Reading frame       0 time 10000.000
Precision of md-nopbc.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
 ->  frame   3500 time 17000.000        ->  frame   3000 time 16000.000
I think the generated trajectory is incomplete because saved frame is incomplete. please guide me.
Many thanks tobest
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