[gmx-users] pbc = xyz with mdrun -pd ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> Hi
> 
> I am setting pbc = xyz ; and type the commands
> 
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 
> 6LYZ-EM-solvated
> 
> mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated
> 
> => the simulation failed and .out file suggested me to use the flag -pd.
> 
> 
> 
> 
> grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 
> 6LYZ-EM-solvated
> mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated
> 
> =>  the simulation runs well.
> 
> 
> Why?
> 

Without a full description of your system, preparation, .mdp options and 
definition of failure (including any relevant error messages), the only answer 
is: absolutely no clue.

-Justin

> 
> Thank you
> Lin
> 
> 
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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