[gmx-users] Speptide - mdrun failed

[David van der Spoel]

montserrat.vaque at urv.cat wrote:
> 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.

that's another mdrun, to do with the OS.

Try to do the following to start with:
source /path/to/GMXRC
(the file is usually in the bin directory of you installation)
> 
> 
> 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.
> 
> Montserrat
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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