[gmx-users] invalid number of nodes

Berk Hess gmx3 at hotmail.com
Wed Aug 13 14:52:30 CEST 2008


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 CVS
which make the tpr files much smaller and large simulations a bit more efficient.


From: regafan at hotmail.com
To: gmx-users at gromacs.org
Date: Wed, 13 Aug 2008 11:51:56 +0000
Subject: [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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