Author Topic: Only one Framework atom taken from .cif file  (Read 380 times)

petersbk

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Only one Framework atom taken from .cif file
« on: April 01, 2019, 04:25:26 PM »
Summary: Large number of FW atoms in .cif file, but simulation only uses 1 of them and at position 0,0,0. What is wrong with .cif or input file?
Warning: Stage 0 Newbie with respect to raspa.

I'm using a bunch of Argon atoms in a P1 40x40x40 box as a "Framework": just a bunch of fixed LJ atoms via the Garcia Perez FF. The simulation attempts gcmc of methane in this framework.  The .cif was made in Avogadro / openbabel after creating the atom positions elsewhere. Here is the top of the .cif:
--------------------------------------------------------------------------------------------
# CIF file generated by openbabel 2.3.2, see http://openbabel.sf.net
data_I
_chemical_name_common 'box6_ar.pdb'
_cell_length_a 40
_cell_length_b 40
_cell_length_c 40
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_space_group_name_H-M_alt 'P 1'
_space_group_name_Hall 'P 1'
loop_
    _symmetry_equiv_pos_as_xyz
    'x,y,z'
loop_
    _atom_site_type_symbol
    _atom_site_label
    _atom_site_Cartn_x
    _atom_site_Cartn_y
    _atom_site_Cartn_z
     Ar   Ar1    19.87500    0.95800   36.89600
     Ar   Ar2    29.92900    6.71600   36.71700
     Ar   Ar3     6.11900    9.36600    1.67600
...
--------------------------------------------------------------------------------------------

And I'm using this simple input file (which started life as one of the Basic examples):

--------------------------------------------------------------------------------------------
SimulationType                MonteCarlo
NumberOfCycles                5000
NumberOfInitializationCycles  1000
PrintEvery                    1000

Forcefield                    GarciaPerez2006

RemoveAtomNumberCodeFromLabel yes
ReadCIFAsCartesian yes
UseChargesFromCIFFile no

Framework 0
FrameworkName box6_ar
ExternalTemperature 300.0
ExternalPressure 1e8

Component 0 MoleculeName             methane
            MoleculeDefinition       TraPPE
            TranslationProbability   0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0
--------------------------------------------------------------------------------------------

When the simulation is run, this is the start of what is printed to stderr:

--------------------------------------------------------------------------------------------
_cell_length_a: 40.000000
_cell_length_b: 40.000000
_cell_length_c: 40.000000
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
space group found from symmetry elements: 1 (nr elements: 1)
unknown: 19.87500
unknown: 0.95800
unknown: 36.89600
unknown: 29.92900
unknown: 6.71600
...
--------------------------------------------------------------------------------------------

There is a separate one of these "unknown" lines for each x, y, and z coordinate in the .cif file.

The simulation runs "fine", but from the _final.pdb etc. files in the Movies directory or from the output, one can see that only one framework atom (@ 0,0,0) was used in the simulation.

What is my problem (at least related to this simulation...)?
Thanks.

Pezhman Zarabadi-Poor

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Re: Only one Framework atom taken from .cif file
« Reply #1 on: April 01, 2019, 06:28:01 PM »
Dear Peter,

I think your issue is coming from the fact that you are providing Cartesian coordinates instead of fractional ones. You may convert it to fractional and then you will have

.
.
.
_atom_site_frac_x
_atom_site_frac_y
_atom_site_frac_z
Ar Ar1 frac_x frac_y frac_z
.
.
.

My best regards,
Pezhman

petersbk

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Re: Only one Framework atom taken from .cif file
« Reply #2 on: April 01, 2019, 07:16:40 PM »
Maybe. The manual says you can use Cartesian coordinates for P1 and I've used the "ReadCIFAsCartesian yes" command in the input file. It is off-topic, but I can't get openbabel to convert this file to fractional coordinates.  Thanks.

Pezhman Zarabadi-Poor

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Re: Only one Framework atom taken from .cif file
« Reply #3 on: April 01, 2019, 09:13:24 PM »
I have not used this option of RASPA but I guess it still needs the CIF in fractional coordinates and then RASPA internally converts it to Cartesian. You may use other software like VESTA to generate CIF in fractional coordinates.

My best,
Pezhman

petersbk

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Re: Only one Framework atom taken from .cif file
« Reply #4 on: April 01, 2019, 11:47:32 PM »
I converted to fractional coordinates by hand, removed the "ReadCIFAsCartesian yes" command, and the same behavior occurs: lots of "unknown" lines to stderr and only one FW atom appears @ 0,0,0. Any other advice? Thanks.

Pezhman Zarabadi-Poor

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Re: Only one Framework atom taken from .cif file
« Reply #5 on: April 02, 2019, 07:39:12 AM »
May you please send your CIF, force field definition, and input file?

petersbk

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Re: Only one Framework atom taken from .cif file
« Reply #6 on: April 02, 2019, 03:15:41 PM »
Thanks for looking into this. The input and .cif files can be taken from my original post (the three atoms shown give similar behavior as a larger number of atoms). This force-field.def file is the one supplied in the latest version of the download. I've done nothing to modify any .def file.

petersbk

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Re: Only one Framework atom taken from .cif file
« Reply #7 on: April 23, 2019, 01:02:41 PM »
In the interest of closure, I'll report that I was only able to solve my .cif file problems by using the header from a working P1 .cif file (e.g. from the structures directory in the distribution), cutting out the coordinates, pasting in fractional coordinates for my system of interest, and modifying the cell parameters. Error messages of the type: "unknown: x" where x is one of the x,y, or z coordinates in the .cif file can occur when something is wrong (not compatible with raspa) with the other lines in the .cif.