[gmx-users] probelm with mdrun

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Mar 15 12:24:20 CET 2005


>      I have added the T-couple parameters.  No problems in running grompp
> tpr and trr files are created sucessfully. But when i run the final mdrun
> simulation it returns
> "Only triclinic boxes with the first vector parallel to the x-axis and the
> second vector parallel to the xy-plane are supported Box(3x3)
> Box [   0]={  nan,  nan, nan}
> Box [   1]={  nan,  nan, nan}
> Box [   2]={  nan,  nan, nan}
> cannot fix pbc"
> What could be wrong Sir.

Maybe your starting structure is not ok.
Have you tried to do a md without t-couple, does it run than?
What is your tau_t value, perhaps you should raise it to 1.0.

> thanks
> bala



 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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