[CP2K-user] Error in Steered Molecular Dynamics
David Figueroa
david.... at gmail.com
Thu Apr 30 20:42:26 UTC 2020
Dear forum I'm trying to perform a QM/MM steered molecular dynamic
simulation. the initial pdb has Na and Cl atoms and firstly I get this
error.
*******************************************************************************
* ___
*
* / \
*
* [ABORT] Unknown element for KIND <NA+>. This problem can be fixed
*
* \___/ specifying properly elements in PDB or specifying a KIND section
or *
* | getting in touch with one of the developers!
*
* O/|
*
* /| |
*
* / \
topology_util.F:1271 *
*******************************************************************************
the I add the Na and Cl element in atom filed ( column 77-78)
but I still has the error message.
Then I add this lines to input file
&KIND NA+
ELEMENT Na
&END KIND
&KIND Cl-
ELEMENT Cl
&END KIND
and calculation runs but I get
*******************************************************************************
* ___
*
* / \
*
* [ABORT]
*
* \___/ CPASSERT failed
*
* |
*
* O/|
*
* /| |
*
* / \
qmmm_init.F:797 *
*******************************************************************************
===== Routine Calling Stack =====
2 qmmm_env_create
1 CP2K
After trying different preconditioners and values EPS_DEFAULT values as
suggested in https://www.cp2k.org/faq:cholesky_decomp_failed
I still get this message, so I think that there is an error in the initial
PDB .
Do you have any recommendations?
Thank you for your time and consideration.
David.
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