[gmx-users] Error of mdrun

[Mark Abraham]

s lal badshah wrote:
> Dear Experts,
> Hi ! I am doing MD simulation on two computer, on one when I want to 
> start the EM and do the mdrun command the following error results:
> 
> linux:~/project # mdrun -v -s em.tpr -c em.pdb
> mdadm: /dev/md-v not identified in config file.
> 
> linux:~/project # mdrun -v -deffnm em
> mdadm: option -d not valid in assemble mode
> linux:~/project #

You are probably using a Linux machine with the mdadm package installed 
- this also contains an mdrun command. This is being found first by the 
PATH environment variable and unsurprisingly it doesn't like your 
options. You could trying juggling the order of the components of your 
PATH variable, or uninstalling mdadm. If you installed GROMACS from an 
rpm, next time pay more attention to the warning messages about conflicts.

Compare "which mdrun" with "which grompp" for further information.

Mark