[gmx-users] Normal Mode

Dan Sponseller gromacs at danpeg.com
Mon Nov 9 00:49:22 CET 2015

Hello everyone.

I am doing a Normal Mode analysis on a small polymer. Just 17 atoms in vacuo. It is well minimized. Norm and Max Force < 1e-4. I am doing the analysis on the full precision configuration using the -t option.

I am getting 6 eigen frequencies and 5 eigenvalues near zero which is of course good. 

However, I am getting 16 eigenfrequencies from 5000 to 21,000 cm-1 with enormous eigenvalues. This does not appear correct. Any insights as to why gromacs is producing these would be appreciated.

Dan Sponseller
PhD candidate
George Mason University.

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