[gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 24 03:59:48 CET 2010

On 24/11/2010 2:22 AM, maria goranovic wrote:
> I have a trajectory containing around 30,000 frames at 20 ps 
> intervals. When I try to read and analyze this trajectory, most gmx 
> tools can read only one frame. I do not know which one.

What did your .mdp file specify for writing? If you wrote (say) 
velocities at 20ps intervals and positions only once, your observations 
are explained. What does gmx_check report?

> For example, g_density will read the entire trajectory, but will 
> finally report that :
> read 1 frame from trajectory. calculating ...

What was the full output?

> When I compress the trajectory to one frame every 500 ps, the gmx 
> tools run fine.

With what command did you compress?

> It seems to be an overflow issue? Is this a bug ? If so, how can it be 
> fixed?

Maybe - but 30,000 frames is not so large that overflow is very 
believable. What GROMACS version?


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