[gmx-users] invalid number of nodes

[Rebeca García Fandiño]

Hello,
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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