[gmx-users] Rerun trajectory does not contain a box

Luca Massaccesi l.massaccesi at univpm.it
Wed Jan 16 17:37:37 CET 2013

Dear gmx users,

Background: I just finished my 100 ns md simulation on a receptor in membrane and I got all my .trr .xtc and .edr output files
In order to calculate the energy potential only for the protein, I made a new .mdp defining  "energygrps : Protein",  thus obtaining a new .tpr for a rerun with mdrun.
The problem is that, if I use the trajectory file "100ns.trr" , the following error message comes out:

Source code file: md.c, line: 626

Fatal error:
Rerun trajectory frame step 50000000 time 100000.000000 does not
contain a box, while pbc is used
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

On the contrary if I use the trajectory file "100ns.xtc" the calculation proceeds with no errors.
I think gromacs reads the box xyz from the coordinate file.
I also know that is better to use the .trr file while rerunnig a calculation, so what do you think could be wrong?

Thank you for your kind help


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