[gmx-users] errors depending on (lack of) solvent

[Anton Feenstra]

gianluca santarossa wrote:

> Dear Users,
> 
> I'm trying to run the gromacs tutorial demo
> /usr/local/share/gromacs/tutor/gmxdemo/demo
> using lammpi on more than one PC.
> Everything works fine if I add water molecules to the system using
> genbox.
> But if I try to run a simulation in vacuo (simply removing the '-cs'
> option from genbox) mpirun exits prematurely:
> 
> MPI process rank 1 (n0, p27449) caught a SIGSEGV.
> MPI process rank 2 (n1, p25070) caught a SIGSEGV.
> MPI process rank 5 (n2, p14853) caught a SIGSEGV.
> MPI process rank 6 (n3, p29311) caught a SIGSEGV.
> [cut]
> 
> This is my script (Every step preciding mdrun_mpi works fine):
> 
> MOL=molecule_name
> 
> pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top
> 
> editconf -f ${MOL}.gro -o ${MOL}.gro -d 1.5
> #genbox -cp ${MOL}.gro  -cs -o ${MOL}_new.gro -p ${MOL}.top     # This
> one works fine
> 
> genbox -cp ${MOL}.gro -o ${MOL}_new.gro -p
> ${MOL}.top                                 # This one doesn't work. It
> lacks '-cs' option
> 
> grompp -np 4 -f em -c ${MOL}_new -p $MOL -o ${MOL}
> 
> mpirun -np 4 /usr/local/bin/mdrun_mpi -nice 4 -s ${MOL} -o ${MOL} -c
> ${MOL}_last -v
> 
> By now I need to run simulations in vacuo, so I cannot use the -cs
> option in genbox.
> Does anyone know the cause of these errors?

You cant split one molecule over multiple processors, remove the -np 4
from grompp commandlines, and run mdrun without mpirun -np4.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|