[gmx-users] invalid number of nodes

Rebeca García Fandiño regafan at hotmail.com
Wed Aug 13 16:12:04 CEST 2008

Thanks a lot for your suggestion.
What I was refering was to this post:
"OR use the 3.3 grompp to produce the mdp files since it will automatically set the fourier grid to fit the number of processors."
Sorry for not explaining it better. 
Anyway, in the new version of Gromacs, the -np option of grompp does not work, does it?
I am new in Gromacs, and I am using a version installed in a common cluster. I don´t know if I could install your modificated version myself.
If I use grompp from the my new version, and I only change fourier_nx and fourier_ny in the input .mdp file, would it be enough to create a correct mdp.out file that works.
Best wishes,
Rebeca García Fandiño
Parc Cientific de Barcelona

From: gmx3 at hotmail.comTo: gmx-users at gromacs.orgSubject: RE: [gmx-users] invalid number of nodesDate: Wed, 13 Aug 2008 14:52:30 +0200

Hi,I don't understand your remark about the mdp file.Where on the wiki does it say something like this?The number of processors is never present in the mdp file.Just use the new version of grompp.A week ago I have committed large changes to the CVSwhich make the tpr files much smaller and large simulations a bit more efficient.Berk.

From: regafan at hotmail.comTo: gmx-users at gromacs.orgDate: Wed, 13 Aug 2008 11:51:56 +0000Subject: [gmx-users] invalid number of nodes

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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