[gmx-users] use particle decomposition: mdrun -pd

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> Hi
> 
> After the two commands,
> grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr
> 
> mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum
> 
> 
> 
> Fatal error:
> pbc type no is not supported with domain decomposition,
> use particle decomposition: mdrun -pd
> 
> 
> 
> What does it mean?
> 

The message is quite clear - you cannot use "pbc = no" with domain decomposition 
(explained in the manual and the Gromacs 4 paper).  You have to revert to using 
particle decomposition with -pd in order to use "pbc = no."

-Justin

> Thank you
> Lin
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================