[gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Nov 10 02:15:37 CET 2014

Dear Users

Firstly thanks (specially Drs. Szilard and Mark ) for helping me out with
the installation of GROMACS 4.6.7 on my university Intel cluster. However I
ran into a new problem while using it.

1. Firstly I used pdb2gmx to process a pdb file.
2. Then I used editconf.
3. Then I used genbox.

But I encountered with the following error.

Initialising van der waals distances...
Will generate new solvent configuration of 5x5x9 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 48600 residues
Calculating Overlap...
box_margin = 0.315
Removed 53454 atoms that were outside the box
OMP: Error #178: Function pthread_getattr_np failed:
OMP: System error #12: Cannot allocate memory

Now upon searching on the web it seems to be an OpenMP error. Again I am in
a fix which I have little or no idea about.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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