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Topics - petersbk

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1
Simulation algorithms and theory / Form of OPLS dihedral potential
« on: October 17, 2019, 03:52:30 AM »

The form of OPLS_DIHEDRAL in the manual (eqn 3.52) and in the code has a constant term: (1/2)p0 and has three 1 +/- cos() terms with periodicities 1,2,3. All of the OPLS dihedral forms I see in the literature have no constant term and either the 3 cos terms or 4. Why the difference? If implementing OPLS FF / molecules, does anyone use the OPLS_DIHEDRAL form or do they use, e.g. the FOURIER_SERIES_DIHEDRAL (with p4 = p5 = 0 and usually p3 = 0 since only a few dihedrals have been published using the periodicity=4 term) form? Am I missing something?

Thanks for any help.

2
General / Status of iRASPA-QT
« on: August 02, 2019, 02:25:56 PM »
The iRASPA-QT project is visible on github. What is the status? Is it usable on linux at this time?
Thanks.

3
Input files and parameters / CIF files help
« on: April 17, 2019, 02:35:56 PM »
What software do people use to successfully manipulate .cif files and get them to work with raspa? I've tried fairly simple things (like read in the FAU_SI.cif provided with raspa, convert it to P1, and export it back to .cif) and they seem to not work; sometimes with useful error messages and sometimes not. Besides Materials Studio which I don't have access to, what software works reliably? I've tried Avogadro and VESTA without success. They usually read each other's exported files or those included with raspa, but raspa does not read theirs. Does anyone have any tricks, hints, reports of idiosyncrasies, recommendations, or things to watch out for?

As an example (but I am really looking for general help), the FAU --> P1 in VESTA exercise above yielded the .cif shown below (and attached), but gave "ERROR in cif-file: no proper space group definition found" (after reporting tons of "unknown" lines) even though it has two lines relating to the space group. (Sorry: I couldn't get attachments to work).

#======================================================================

# CRYSTAL DATA

#----------------------------------------------------------------------

data_VESTA_phase_1


_chemical_name_common                  'FAU'
_cell_length_a                         24.34500
_cell_length_b                         24.34500
_cell_length_c                         24.34500
_cell_angle_alpha                      90
_cell_angle_beta                       90
_cell_angle_gamma                      90
_space_group_name_H-M_alt              'P 1'
_space_group_IT_number                 1

loop_
_space_group_symop_operation_xyz
   'x, y, z'

loop_
   _atom_site_label
   _atom_site_occupancy
   _atom_site_fract_x
   _atom_site_fract_y
   _atom_site_fract_z
   _atom_site_adp_type
   _atom_site_B_iso_or_equiv
   _atom_site_type_symbol
   O1         1.0     0.895800      0.104200      0.000000     Biso  1.000000 O
...

Thanks for any help.

4
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.

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