Orbital Transformation

Sudip Das das.s... at gmail.com
Sat May 5 13:32:41 UTC 2018

Dear All,

I am trying to reproduce the following article:

Free Energy Barriers for the N-Terminal Asparagine to Succinimide
Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated
Model; Kaliman *et al.; *JCTC 2010, 6, 184-189.

As of now, I am trying to run the BOMD equilibration step in CP2K. For
orbital transformation, the authors had used a method described in the
following article:

VandeVondele, J.; Hutter, J. J. Chem. Phys. 2003, 118, 4365-4369.

According to this method, how does the OT section of my CP2K input file
look like? Especially what MINIMIZER and PRECONDITIONER should I use?
According to my understanding, I tried to use DIIS as minimizer and
FULL_SINGLE as the preconditioner. When a submitted the job in 2 nodes, it
came with the following error:

*   ___
 *  /   \
 * [ABORT]
 *  \___/    Cholesky decompose failed: the matrix is not positive definite
or *
 *    |                              ill-conditioned.
 *  O/|
 * /| |
 * / \
fm/cp_fm_cholesky.F:94 *

So, I tried with following two options separately:

1) with "CHOLESKY OFF"
2) with CG minimizer and FULL_SINGLE_INVERSE preconditioner,

but in both cases, I got the same error as previous.

Furthermore, when I tried to submit the job in a single node, it ran, but
after 1.7 ps, some bonds broke which is not at all expected.

What could be the reason(s) behind all these anomalies? Any help would be
greatly appreciated.

By the way, I ran all these simulations in CP2K 4.0 with GPU acceleration.

Thanks in advance,

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India
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