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Hi CP2K group,
I am trying to create a PSF file for ALOOH surface. I have a particular
requirement that the psf file should have connections shown as in left
figure.
I have created the PSF file, but CP2K shows error:
CP2K requires molecules to be contiguous and we have detected a non *
* [ABORT] contiguous one!! In particular a molecule defined from index
( *
* \___/ 1) to ( 210) contains other molecules, not connected!
My PSF file look like this:
256 !NATOM
1 14 01 DIAS Al1 YA 0.000000 0.0000 0
2 14 01 DIAS Al2 YA 0.000000 0.0000 0
3 03 01 DIAS Al3 YA 0.000000 0.0000 0
4 03 01 DIAS Al4 YA 0.000000 0.0000 0
5 13 01 DIAS Al5 YA 0.000000 0.0000 0
6 13 01 DIAS Al6 YA 0.000000 0.0000 0
7 02 01 DIAS Al7 YA 0.000000 0.0000 0
8 02 01 DIAS Al8 YA 0.000000 0.0000 0
9 12 01 DIAS Al9 YA 0.000000 0.0000 0
10 12 01 DIAS Al1A YA 0.000000 0.0000 0
11 01 01 DIAS Al1B YA 0.000000 0.0000 0
Questions:
1) If it is same molecule, then in PSF file should SEGMENT ID should be
defined exactly in a row? for instance
which format is correct for CP2K. See SEGMENT ID (second column).. Should
each molecule be defined in a row or it can be expressed randomly?
256 !NATOM
1 AA 01 DIAS Al1 YA 0.000000 0.0000 0
2 BB 01 DIAS Al4 YA 0.000000 0.0000 0
3 AA 01 DIAS Al3 YA 0.000000 0.0000 0
4 AA 01 DIAS Al2 YA 0.000000 0.0000 0
5 BB 01 DIAS Al5 YA 0.000000 0.0000 0
256 !NATOM
1 AA 01 DIAS Al1 YA 0.000000 0.0000 0
2 AA 01 DIAS Al2 YA 0.000000 0.0000 0
3 AA 01 DIAS Al3 YA 0.000000 0.0000 0
4 BB 01 DIAS Al4 YA 0.000000 0.0000 0
5 BB 01 DIAS Al5 YA 0.000000 0.0000 0
2) In my current ALO(OH), except for the non-hydroxy oxygen everything are
connected. I could create PSF connecting all atoms (easier to create for me
compared to the PSF separating the non-hydroxy oxygen). Is there any easier
way to define non-hydroxy oxygens as separate molecules, so that I can have
1-3 VdW, EI.
Please let me know. Attached are my PSF, input and PDB files.
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