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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