[gmx-users] Speptide - mdrun failed

montserrat.vaque at urv.cat montserrat.vaque at urv.cat
Tue May 9 09:20:25 CEST 2006

Dear All,

I'm just getting started with GROMACS. I configured and installed fftw-3.0.1 and then I configured, compiled and installed gromacs-3.3.1.tar.gz as INSTALL file showed.
I thought that the installation had been successful and I performed the simulation of the peptide (speptide, the one the example proposed).

I executed:

1) pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro

2) editconf -f speptide -o -d 0.5

3) genbox -cp out -cs -p speptide -o b4em

4) grompp -v -f em.mdp -c b4em -o em -p speptide

Theses steps didn't give me apparent problems. But when I executed:

mdrun -v -s em -o em -c after_em -g emlog

This message appeared:

mdadm: /dev/md-v not identified in config file.

I don't understand what it means. I would appreciate some suggestions to continue the example. I am not able to find the answer about it.

Thank you for your help in advance.

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