Rigid body simulation

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Azamat Rizuan

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Jul 18, 2021, 2:23:39 AMJul 18
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Greetings,

I was trying to simulate fully rigid proteins using HOOMD. For that, I have tried to test a simpler system first. It is a system of  three triangular molecules sitting on each other (see picture). My plan was to use LJ potential so I have calculated an analytical solution for this system. So, it was equal to -0.6341327 kcal/mol after excluding intramolecular interactions. 

Then, I have created this system with 6 particles in HOOMD. In HOOMD, I have also created 2 central particles with required properties (tag, body, moment of inertia, orientation, mass etc.) and defined rigid chains as below:


rigid = hoomd.md.constrain.rigid();
rigid.set_param('2',
                types=['1']*3,
                positions=[(0,0,0),(1,1,0),
                            (2,0,0)])
rigid.set_param('3',
                types=['1']*3,
                positions=[(0,0,1),(1,1,1),
                            (2,0,1)])
rigid.create_bodies(False)


When I run this fully rigid case, I am getting some discrepancy in potentials between HOOMD and my analytical solution. The pair_lj_energy from HOOMD was  -0.258301451 kcal/mole. 
Could you please help me with this issue? I have attached my HOOMD simulation file (run_rigid.py). Thanks in advance.

Best,

Azamat
triangular system.png
rigid_compare.zip

Joshua Anderson

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Jul 19, 2021, 12:33:16 PMJul 19
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Azamat,

You state that you have an analytical solution, but you do dot define the problem. What problem is -0.6341327 the solution to?

Also, note that you only need one type of rigid body in your system. Use the parameters for the '2' type and move the second body by changing the particle's position.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
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> <triangular system.png><rigid_compare.zip>

Azamat Rizuan

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Jul 21, 2021, 11:28:10 AMJul 21
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Thanks, using one type for the central particle and shifting constituent particles for the second rigid body helped me. Currently, I was able to match my numerical results with HOOMD.

Best,

Azamat
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