Henglu Xu¹, Raffaela Cabriolu^2*, Berend Smit^1*

1 Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1951 Sion, Valais, Switzerland

2 Department of Physics, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D5-149, 7491 Trondheim, Norway

* Corresponding authors emails: raffaela.cabriolu@ntnu.no, berend.smit@epfl.ch

DOI10.24435/materialscloud:9w-gz [version v1]

Publication date: Jan 26, 2022

How to cite this record

Henglu Xu, Raffaela Cabriolu, Berend Smit, On the effects of the degrees of freedom on calculating diffusion properties in nanoporous materials, Materials Cloud Archive 2022.13 (2022), doi: 10.24435/materialscloud:9w-gz.

Description

If one carries out a molecular simulation of N particles using periodic boundary conditions, linear momentum is conserved and hence the number of degrees of freedom is set to 3N-3. In most programs, this number of degrees of freedom is the default setting. However, if one carries out a molecular simulation in an external field, one needs to ensure that degrees of freedom are changed from this default setting to 3N, as in an external field the velocity of the center of mass can change. Using the correct degrees of freedom is important in calculating the temperature and in some algorithms to simulate at constant temperature. For sufficiently large systems, the difference between 3N and 3N-3 is negligible in the way. However, there are systems in which the comparison with experimental data requires molecular dynamics simulations of a small number of particles. In this work, we illustrate the effect of an incorrect setting of degrees of freedom in molecular dynamic simulations studying the diffusion properties of guest molecules in nanoporous materials. We show that previously published results have reported a surprising diffusion dependence on the loading, which could be traced back to an incorrect setting of the degrees of freedom. As the correct settings are convoluted and counter-intuitive in some of the most commonly used molecular dynamics programs, we carried out a systematic study on the consequences of the various commonly used (incorrect) settings. Our conclusion, is that for systems smaller than 50 particles the results are most likely unreliable as these are either performed at an incorrect temperature or the temperature is incorrectly used in some of the results. Furthermore, a novel and efficient method to calculate diffusion coefficients of guest molecules into nanoporous materials at zero loading conditions is introduced.

Materials Cloud sections using this data

Files

File name	Size	Description
README.md MD5md5:50129b1059b5fc938682217eaadfb71d	1.8 KiB	Description of attached files of LAMMPS inputs in SI
example_casestudy_1_MgMOF74_NP14.tar.gz MD5md5:fed082a2dba46d4210ed8390f9862598	100.0 KiB	One example of LAMMPS inputs files for case study 1
example_casestudy_2_HKUST1_NP16.tar.gz MD5md5:bd8edbb288b641fabf978b0204b90e6d	50.0 KiB	One example of LAMMPS inputs files for case study 2
example_casestudy_3_FAU_12UC.tar.gz MD5md5:067100af1c43313da00d61cd1ae91168	50.0 KiB	One example of LAMMPS inputs files for case study 3
example_casestudy_4_FAU_NP160.tar.gz MD5md5:674ec7c23cdad7f3e4a44846a5d49798	360.0 KiB	One example of LAMMPS inputs files for case study 4
all_casestudy_1_MOF74.tar.gz MD5md5:9fa11d0786662327f084c55b9df23d9d	5.4 MiB	All LAMMPS inputs files for case study 1
all_casestudy_2_HKUST1.tar.gz MD5md5:5b5a35b5b6fb9d336b387e34ffedf30c	2.0 MiB	All LAMMPS inputs files for case study 2
all_casestudy_3_zeolites.tar.gz MD5md5:56b8c6a36bfb3dfe6594671d00c676d5	7.5 MiB	All LAMMPS inputs files for case study 3
all_casestudy_4_zeroloading.tar.gz MD5md5:0bee05ef4018dea8772af286580fd904	15.5 MiB	All LAMMPS inputs files for case study 4

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External references

Keywords

molecular dynamics simulation diffusion nanoporous materials SNSF MARVEL PRACE metal-organic frameworks zeolites