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Output files / Re: Visualization of adsorption
« Last post by David Dubbeldam on December 09, 2019, 08:54:35 AM »
You just import all the pdb- and cif-files you would like to visualize (so select multiple files during import).
Then you can set individual visualization properties, like origin, drawing-method, etc.
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Input files and parameters / Re: TraPPE-EH force field in molecule definitions
« Last post by David Dubbeldam on December 05, 2019, 04:28:53 PM »
Either use a model that puts the charge-centers on the atomic centers (OPLS) or if the molecule is small you can also make the whole molecule rigid.
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General / Re: Flexible-MOFs forcefield Issue
« Last post by YangLZ on November 15, 2019, 12:39:59 PM »
Thanks for your response.  :)
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General / Re: Flexible-MOFs forcefield Issue
« Last post by David Dubbeldam on November 08, 2019, 04:13:47 PM »
For a force field for a flexible MOF you need to define all the interactions similar to the flexible IRMOF-1 example.
The GenericMOFs defines only the interactions of molecules with the framework.
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General / Flexible-MOFs forcefield Issue
« Last post by YangLZ on November 04, 2019, 03:03:52 PM »
Dear Prof. Dubbeldam,

Is it OK to use the genericMOFs Forcefield to optimize a flexible-MOFs? Or every flexible-MOFs need a specific Forcefield, just like Dubbeldam2007FlexibleIRMOF-1 for IRMOF-1and Dubbeldam2007FlexibleIRMOF-10 for IRMOF-10?

Kind regards,
YangLZ
6
Input files and parameters / TraPPE-EH force field in molecule definitions
« Last post by GIV on October 23, 2019, 01:25:25 PM »
Hello Prof. Dubbeldam,

I would like to use TraPPE – Explicit Hydrogen model to define a flexible di-n-propylamine molecule. For TraPPE-EH alkane models interaction sites for hydrogen are shifted from the atomic nuclei out to the C-H bond center. I would like to ask how can I set dummies in a molecule definition file?

Kind regards,
Ivan
7
Input files and parameters / Re: Charge equilibration for MOFs
« Last post by ignas on October 18, 2019, 11:57:45 AM »
Hi,

thank you very much for your remark! So, in case when the number of framework atoms in output file and in cif do not match what could be done? As well, I noticed that program destroys the MOF connectivity in Framework_0_final_1_1_1.cif file. Only final P1 file contains proper connectivity.
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Input files and parameters / Re: Charge equilibration for MOFs
« Last post by Kajum Safiullin on October 18, 2019, 11:15:12 AM »
I would suggest first to check the cif and the header of the output file (framework atoms lines) of the simulation if they state the same number of atoms in your cell. Once I used a quite large cell and amount of atoms was surprisingly reduced if compared with the input structure file.
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Input files and parameters / Charge equilibration for MOFs
« Last post by ignas on October 17, 2019, 03:52:03 PM »
Hi,

I did used RASPA for UiO-66 MOF charge equilibration. In the output file for ChargeEquilibration the net charge was 0. I used the generated Framework_0_final_1_1_1_P1.cif for adsorption calculations. The error message I have got was 'WARNING: THE SYSTEM HAS A NET CHARGE' . For adsorption simulation I used standard input file as for MOF examples.
I was wondering whether I have made a mistake during the charge equilibration or simulation?

Kind regards,
Ignas
10
Input files and parameters / Re: Blocking pockets in MD?
« Last post by Kajum Safiullin on October 17, 2019, 10:38:26 AM »
Thank you for the information.
I am using raspa for a somewhat different than a gas in zeolite-like structures with closed pores, the system and its conditions are different to ones usually used in raspa simulations. However I found raspa as a nice code that suits my basic requirements for simple initial tests of a complicated system after some modifications of my structure with a side-pocket (as you called it). I'll think on new mods to solve my problem with MD.
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