[gmx-users] invalid number of nodes

Rebeca García Fandiño regafan at hotmail.com
Wed Aug 13 13:51:56 CEST 2008

I want to simulate a membrane+proteína system  (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc.
I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version.
For grompp with Gromacs 3.3 I amincluding this options in the input mdp file:

fourierspacing           = 0.12
fourier_nx               = 1024
fourier_ny               = 1024
fourier_nz               = 0

but when I execute:

grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512
I receive this error:
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1021
Fatal error:
invalid number of nodes 512

When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear.
Is there a limit of processors in Gromacs for grompp or which could be the problem?
Thank you very much for your help in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
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