Restarting rigid body simulations, molecules breaking up

[Ramanish Singh]

Hi,

I want to simulate a box of rigid molecules at a fixed density and temperature.

I first start with a very big box with the desired number of molecules, shrink it to the desired density and save the last frame. I then use that frame to start an NVT MD simulation.  The problem is that my rigid bodies are breaking up in the NVT simulatin (i.e. I do not know how to make them rigid in the NVT simulation).

The manual says : " You still need to specify the same local body space environment to rigid as you did in the earlier simulation". But I am not able to understand how to execute it.

I have attached my python files.

shrink-md.py : Generates the system and brings it to the target density

md.py : NVT MD file that uses out-shrink.gsd to create initial structure

Thanks.

Thanks,

Ramanish

[Joshua Anderson]

Ramanish,

You are missing the `constrain.rigid` and the relevant parameters in your `md.py` file. This is what defines the rigid bodies.

rigid = hoomd.md.constrain.rigid();
rigid.set_param('V',
types=['CH3']*2,
positions=[(-0.106,0,0),(0.106,0,0)],
charges=[0,0])
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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> <md.py><shrink-md.py>

[Ramanish Singh]

Thanks Josh!