[gmx-users] (no subject)

[Mark Abraham]

Sunil Thapa wrote:
> Respectable Mark/Berk/David
> I am trying to study diffusion of oxygen in water at a constant pressure 
> of 1 bar. When I run the production run of 1 ns then I get an warning 
> message as follows and the run terminates. Please try to figure out what 
> might have been wrong.
>  
> Grid: 35 x 35 x 35 cells
> WARNING: your box is exploding! (ncells = 42875)

There's the main problem. See http://wiki.gromacs.org/index.php/blowing_up

>            Step           Time         Lambda
>           17200       34.40000        0.00000
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         1.000000      1      2   1.000000
>         After LINCS         1.000000      1      2   1.000000

The line below is some other issue.

> Fatal error: Can not read/write topologies to file type unknown

Mark