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Re: Rod shape particle

From: Ahmad Reza Motezakker
Subject: Re: Rod shape particle
Date: Tue, 9 Feb 2021 06:48:02 +0000

Dear Rudolf/Dear Salvador,

Thank you very much for your constructive comments. I will try both of ideas.

Moreover, I have realised that RATTLE algorithm needs small time step (faster) to converge.

Best regards,

Ahmad Reza 

From: Rudolf Weeber <>
Sent: Monday, February 8, 2021 8:39:08 PM
To: Ahmad Reza Motezakker
Subject: Re: Rod shape particle
Hi Ahmad,
On Thu, Jan 28, 2021 at 09:17:36AM +0000, Ahmad Reza Motezakker wrote:
> I am trying to create rod shape particles with the help of creating polymer and defining rigid bonding between the particles. Although I have decreased the tolerance for position and velocity, when I visualize the particle, it is clear that it does not act like a rod and it bends.
Please be aware that the RigidBond (using thre RATTLE algorithm) only controls distances, not any angles between vectors connecting partiles.
For a bunch of particles placed in a straight line p1-p2-p3-...-p9,
adding a rigid bonds p1-p2 p2-p3 p3-p4 will not do the trick. E.g., while keeping all distances, p3 could rotate around the p1-p2.
If you want to stay with RigidBonds, you can use two rigid bonds one of length l and one of length 2l and do
p1-p2 (l) p1-p3 (2l) p2-p3 (l) p2-p4 (2l) ...

Alternatively, please use the VirtualsSitesRelative feature as explained in the raspberry tutorial (preferred method):
* Place an odd number of particles in a straight line
* Turn on rotation on the middle particle
* on all particles except the middle one, call vs_auto_relate_to() to relate them to the middle one.

Hope that helps!
Regards, Rudolf

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