[gmx-users] Normal Mode Analysis failing with no error message
cyberjhon at hotmail.com
Tue Aug 30 22:55:42 CEST 2016
I am trying to do a Normal Mode Analysis on a protein assembly with 1.05 million atoms
without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double precision
using 1024 processor and up to 256 GB of RAM, but it always fails.
I do not get any error message from Gromacs in just finished.
The last lines of my error log file are:
starting normal mode calculation 'GRoups of Organic Molecules in ACtion for Science in water'
Maximum force: 1.59067e+03
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.
[NID 00841] 2016-08-30 16:36:59 Apid 6732636: initiated application termination
[NID 00841] 2016-08-30 16:37:01 Apid 6732636: OOM killer terminated this process.
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