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Input files and parameters / TraPPE-EH force field in molecule definitions
« Last post by GIV on Today at 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
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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
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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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Simulation algorithms and theory / Form of OPLS dihedral potential
« Last post by petersbk 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.
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Input files and parameters / Re: Blocking pockets in MD?
« Last post by petersbk on October 17, 2019, 03:41:33 AM »
Hello Kajum,

It seems to me that block pockets only has an effect during Monte Carlo moves. So, in an MD simulation, when raspa is initially adding molecules to a framework to give the desired number, it will not allow their creation in blocked pockets. During MD however, if a molecule is able get into a pocket (a "side-pocket"), it will spend time there.

Why would want to block pockets in MD if the molecules are able to move into the pockets under normal circumstances given the structure, the force-field, and the conditions?

Blocking pockets is normally done on isolated pockets that don't communicate with accessible channels. If you want to block regions of a framework that are actually accessible during MD, then you have to decide where the boundary of the pocket is and your results will depend on the exact nature of what you block with. The blocking of isolated pockets during MC is somewhat different. If you fill the pocket with a hard-sphere, there will be a range of hard spheres that all give the same effect and do not modify anything happening outside the pockets.
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Input files and parameters / Blocking pockets in MD?
« Last post by Kajum Safiullin on October 16, 2019, 03:42:04 PM »
Hi everyone,

I have to use blocking pockets in both MC and MD simulations. It works fine with MC, but doesn't work during MD simulations at all: gas molecules keep going inside the blocked pockets (they have open geometry in my case and are not surrounded by framework atoms). Any ideas how to solve this issue?

I will appreciate any help.
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Output files / Visualization of adsorption
« Last post by RAHMA on October 10, 2019, 02:45:45 PM »
Dear iRaspa developers,

I am trying to visualize the adsorption of CO2 in MOF through the option "Movie" in simulation input but i didn't know how to do it with iRaspa ....
Could you please help me with some detailed instructions to visualize the CO2 inside the MOF i already generated the cif and pdb files after the adsorption of CO2.

Thank you !

Rahma.
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Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites
« Last post by David Dubbeldam on October 04, 2019, 01:18:16 PM »
You could do some basic debugging, like setting the PrintEvery to 1 and see if it is just slow or that you are really stuck at step 0.
The latter can happen if you try to put in more molecules than fit in the simulation volume.
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