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General / How to get movie from MD
« Last post by sara abbasi on June 07, 2022, 08:15:40 PM »
Dear Prof. Dubbeldum

Is there any method to get movies from MD results to show that the molecules with higher diffusion coefficient have higher speed in the framework than molecules with lower diffusion coefficient?
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General / Re: LAMMPS.trj file to cif
« Last post by bphan on June 06, 2022, 05:53:49 PM »
Nice! That was the final piece to make this work. thank you so much.
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Hi everyone

I start learning RASPA recently by the manual and examples in the RASPA, but I get confused about the definition of radii in the pseudo_atom.def file. In the examples in RASPA, for CO2, C_co2 is 0.72 and O_co2 is 0.68. For tip5p water,  Ow is 0.5 and Hw is 1.0. I cannot understand why those values are set. If the unit of radii is Angstrom? In the community forum, Dr. Dubbeldam explained that it is  relative position of all atoms, but I still cannot understand it. Could you possibly give more detailed explanation about how to define radii in the pseudo_atom.def? For small rigid molecules, Could I not give the radii or just set all them to 1.0. Your help is appreciated.
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General / Re:negative MSD slope
« Last post by David Dubbeldam on June 04, 2022, 07:06:06 PM »
See literature on how to compute diffusion coefficients from MSD. The slops of the MSD at long times can not be negative.
You're probably looking at a situation where MD is not capable of computing diffusion because it is too slow.
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General / Re:negative MSD slope
« Last post by sara abbasi on June 04, 2022, 04:50:05 PM »
Dear Prof.Dubbeldum

I calculated diffusion coefficient for a binary mixture. The slope of MSD is negative and therefore diffusion coefficient is negative ( for example slope= -0.014 for one or both of species ). Could you please explain the physical meaning of that observation?
I will be so grateful if you guide me.
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General / Re: LAMMPS.trj file to cif
« Last post by David Dubbeldam on June 02, 2022, 05:44:08 PM »
About the gif-file: The _atom_site_type_symbol needs to be the chemical element. The _atom_site_label is used in the forcefield definition as a label of the atom.
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General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 31, 2022, 11:46:34 PM »
Also when i have more complicated systems there'll be for example, carbons with different LJ potentials, so like c3 and ca that I would have to input, how would i input them so it won’t be overwritten?
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General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 31, 2022, 11:37:15 PM »
Is the problem with how my cif file is set up?
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General / Re: LAMMPS.trj file to cif
« Last post by bphan on May 31, 2022, 11:07:09 PM »
Ah ok, this is making a lot more sense.
I have the mixing force fields and pseudo atoms defined, and the calculations are generating different values for the Henrys constant now though, so most things are working right. 
But im running into the problem of not seeing my hc and c3 being included in the mixing rules. Attached are the inputs.
I think the c3 is being overwritten by the C? Should i just change the potential of C to c3?
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General / Re: LAMMPS.trj file to cif
« Last post by David Dubbeldam on May 31, 2022, 04:35:26 PM »
All atom-types need to be defined in the 'pseudo_atoms.def', so 'c', 'c3', 'hc', but also all atoms of the probe molecule.
Next define LJ parameters all of these for 'force_field_mixing_rules.def'.
The mixing rules with the be used to computed cross-interactions between all of the atoms.

You seems to have placed them in 'force_field.def' which is means to overwrite interactions for systems where mixing rules are not applicable. But these are no interactions defined then between {'c', 'c3', 'hc'} and all of the adsorbate atoms of the probe molecules.
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