Restart with atom kind error

[Amami Haruka]

I tried to continue the simulation with restart file with cp2k8.1. The first simulation starts from a PDB coordinate file and finished normally. 

However, the new simulation gives Unknown element for KIND <HX1> error. when reading the restart file, even though no PDB file is being provided.

The first simulation is run with the command cp2k.sopt monitor.inp > monitor.out.

The second simulation is run with the command cp2k.sopt metaD.inp > metaD.out.

The input and out files are attached.

[Amami Haruka]

Sorry, there seems to be a problem with attaching files.

[Amami Haruka]

Ok, I solved the problem.

If your input file has an unusual atom mapping. For example, a proton in your ligand has atom name HX.

cp2k could only recognise this mapping from HX to H, if both the topology file and coordinate file are provided.

So you would need

    &TOPOLOGY

      CONN_FILE_FORMAT AMBER

      CONN_FILE_NAME MM.prmtop

      COORD_FILE_NAME npt.pdb

      COORD_FILE_FORMAT PDB

    &END TOPOLOGY

and this won't work.

    &TOPOLOGY

      CONN_FILE_FORMAT AMBER

      CONN_FILE_NAME MM.prmtop

    &END TOPOLOGY

Given that the amber topology contains this mapping information, I think it would be more useful if the cp2k could read this mapping information when only CONN_FILE is provided.

In cp2k-8.1/src/topology_util.F, SUBROUTINE check_subsys_element(element_in, atom_name_in, element_out, subsys_section, use_mm_map_first) doesn't seems to do this.

[Amami Haruka]

adding the missing atoms seems to give another problem.

The original simulation runs fine for a very long time. 

cp2k.psmp equil.inp > equil.out

However, restart the simulation with the same file gives

cp2k.psmp test.inp > test.out

  Translating the system in order to center the QM fragment in the QM box.

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 *   ___                                                                       *

 *  /   \                                                                      *

 * [ABORT]                                                                     *

 *  \___/                             CPASSERT failed                          *

 *    |                                                                        *

 *  O/|                                                                        *

 * /| |                                                                        *

 * / \                                                  cp_ddapc_methods.F:652 *

 *******************************************************************************

 ===== Routine Calling Stack ===== 

            9 ewald_ddapc_pot

            8 cp_ddapc_create

            7 cp_ddapc_init

            6 qs_env_update_s_mstruct

            5 qs_energies_init_hamiltonians

            4 qs_energies

            3 qs_forces

            2 qs_mol_dyn_low

            1 CP2K

[Václav Havel]

Hi

Have you solved this problem?

I also meet that  CPASSERT failed

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 *   ___                                                                       *

 *  /   \                                                                      *

 * [ABORT]                                                                     *

 *  \___/                             CPASSERT failed                          *

 *    |                                                                        *

 *  O/|                                                                        *

 * /| |                                                                        *

 * / \                                                      qmmmx_update.F:193 *

 *******************************************************************************

Best 

Vaclav