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From: | Ahmad Reza Motezakker |
Subject: | Fw: Particle size and time scale |
Date: | Tue, 2 Mar 2021 10:42:55 +0000 |
From: Ahmad Reza Motezakker
Sent: Tuesday, March 2, 2021 11:40 AM To: Peter Košovan Subject: Re: Particle size and time scale Dear Peter,
Thank you very much for the reply. Exactly as you mentioned, I compare MSD and diffusion of the rod shape particle with the famous theories of stiff polymer physics in books and papers (for example, Doi and Edwards, Odijk and ...). I have checked most of the papers which espressoMD (CG+LBM) has been used in them and to my knowledge, they have not mentioned the way that they have defined the time scale. I really be thankful if you give me some hints on considering viscosity in calculating time scale or any paper. Thank you.
Best regards, Ahmad Reza From: Peter Košovan <peter.kosovan@natur.cuni.cz>
Sent: Tuesday, March 2, 2021 11:22:26 AM To: Ahmad Reza Motezakker Subject: Re: Particle size and time scale Dear Ahmad,
Please, be aware that in implicit-solvent simulations you cannot simply calculate the time scale by calculating the unit of time from the simulation units of mass, energy and length. The reason is that the implicit solvent (or LBM coupling in your case)
determines the viscosity of the solvent, which does not enter in the calculation of the time unit. Therefore, dynamics in CG simulations is accelerated. In other words, your actual time unit is several orders of magnitude greater than what you get from simple
conversion of units.
You can calculate your dynamical time scales by measuring the diffusion coefficient of a single particle with the same parameters.
It might be also helpful if you specify the theory to which you are comparing your results.
With regards,
Peter
On Tue, Mar 2, 2021 at 11:13 AM Ahmad Reza Motezakker <armot@kth.se> wrote:
-- Dr. Peter Košovan
Department of Physical and Macromolecular Chemistry Tel. +420221951029 Fax +420224919752
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