[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.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200430/162af70c/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Reac_ME6.pdb
Type: application/vnd.palm
Size: 3320804 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200430/162af70c/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: SMD_ME6.qmmm
Type: application/octet-stream
Size: 5688 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200430/162af70c/attachment.obj>


More information about the CP2K-user mailing list