[gmx-users] box size with pressure coupling

[Anton Feenstra]

"Lynne E. Bilston" wrote:
> 
> Hi all,
> 
> Maybe I'm missing something obvious here, if so please enlighten me.

[..snip..]

> The weird thing is that despite using the coordinates (-c pdb file) and the
> trajectory ( -t trr file) from after the  equilibration, the box size at
> the start of the second pressure coupled run resets itself to the size
> before the original pressure coupled run. Is grompp taking the coordinates
> (and thus box size) somehow from the first frame of the trajectory instead
> of the last as specified in the manual?  To summarise, I am doing the
> following:

grompp takes "The last frame with coordinates and velocities", so maybe
you didn't write out any velocities to your .trr file? You can check
that using 'gmxcheck -f traj.trr'. Also, you should check the output
of grompp. It usually says exactly what it does, although I must concur
that it is easy to miss something among al the jumbled messages...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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