[gmx-users] not allocate memory and genconf

saly jackson saly.jackson12 at gmail.com
Fri Mar 9 17:02:46 CET 2012

Hi Justin

According to the following you said that I should use genconf. Would you
please help me to use it?

Would you please tell me instead of the following command:

genbox -ci H.gro -nmol 80000 -box 300 300 300 -p topol.top -o H-box.gro

Which command I should use including genconf and genbox as you said.


> Hi
> I think the error is not a reason of less memory of my computer. Because
> in a supercomputer I see the hollowing error too.

genbox is not parallelized, and thus cannot make use of multiple processors
the memory on them.

> Genbox could be run if I choose the number of atoms less than 5000.

The fact that you can add 5000 molecules but not 80000 suggests that
insufficient memory is precisely the problem.  Gromacs is even telling you
in the fatal error below.

Please refer to the solution I proposed earlier.  It is a more robust
than what you're trying to do.

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