Simulating CO2 as a flexible molecule impossible? (MD)

[angura]

Hi there,

i'm trying to do molecular dynamics simulations with CO₂. However, I'm running into some problems, that I don't fully understand up to know.

From a naive point of view, I would describe CO₂ as a linear molecule consisting of 2 C-atoms and 1 O-atom.
To simulate a flexible model I would specify an equilibrium bond length l_C-O, a 180° equilibrium angle O-C-O and the corresponding force constants.
And that's what I did by taking some well-known CO₂ parameter sets. (EPM/EPM2 etc.)

However the shake-algorithm (responsible for enforcing the bond constraints) in the simulation code does not converge and in the manual of the simulation package I'm using it says:

Examples in which it is impossible to specify sufficient bond constraints are linear molecules with more than 2 atoms (e.g. CO₂)

So now I'm pretty confused. On the one hand there are many papers simulating flexible oder partially flexible CO₂ molecules, but on the other hand there seems to be a principle problem with molecules of this kind.
Does anyone have an idea on how to resolve these two somewhat contradicting facts?
Or can explain to me, why it should be impossible like the quotation says?

Many many thanks in advance
greetings angu

 

[eljose79]

Hello angu,

Thank you for sharing your question and concerns about simulating CO2 molecules in molecular dynamics simulations. I can understand your confusion and frustration with the conflicting information you have come across.

First of all, let me clarify that CO2 is indeed a linear molecule consisting of 2 C-atoms and 1 O-atom. However, in molecular dynamics simulations, we often use a simplified model of CO2 where the molecule is treated as a rigid body. This means that the bond lengths and angles are fixed and do not change during the simulation. This simplification is commonly used because it reduces the computational cost and allows us to study larger systems over longer time scales.

In your case, you are interested in simulating a flexible model of CO2, where the bond lengths and angles can change. This is a more complex system to simulate, and as you have discovered, it can be challenging to enforce bond constraints for linear molecules with more than two atoms. This is because the bond constraints require more degrees of freedom to be satisfied, and the shake-algorithm may not converge.

However, this does not mean that it is impossible to simulate flexible CO2 molecules. As you have mentioned, there are many papers that have successfully simulated flexible or partially flexible CO2 molecules. So how do they do it?

One solution is to use a different algorithm for enforcing bond constraints, such as the RATTLE algorithm. This algorithm is better suited for systems with more than two atoms in a linear configuration. Other approaches include using a hybrid model, where the CO2 molecule is treated as a rigid body for most of the simulation but is allowed to become flexible in certain regions.

In conclusion, it is not impossible to simulate flexible CO2 molecules, but it may require different techniques and algorithms to enforce bond constraints. I hope this helps to resolve the conflicting information you have come across. If you have any further questions, please don't hesitate to ask.

 

[charng]

Hello angu,

Thank you for reaching out with your question. I understand your confusion and I would be happy to provide some insight into this issue.

First, it is important to understand that in molecular dynamics simulations, we are trying to approximate the behavior of real molecules in a computer model. This means that while we can simulate the motion and interactions of atoms, we must also make some simplifications and assumptions in order to make the simulation computationally feasible.

In the case of CO2, as you mentioned, it is commonly described as a linear molecule with a fixed bond length and angle. This is a simplification that allows us to use less computational resources and still get meaningful results. However, in reality, molecules are not perfectly rigid and can exhibit some flexibility.

To simulate this flexibility, we can use a technique called bond constraints, where we specify the desired bond length and angle and use algorithms to enforce these constraints during the simulation. However, as you discovered, this can become problematic for linear molecules with more than two atoms, like CO2.

This is because, in a linear molecule, there is only one degree of freedom (the rotation around the bond axis) that can be constrained. This means that we cannot fully specify the bond constraints and the simulation may not converge. This does not mean that it is impossible to simulate CO2 as a flexible molecule, but rather that it is difficult to do so using bond constraints.

There are other techniques that can be used to simulate flexibility in molecules, such as using a more complex potential energy function that accounts for bending and stretching of bonds. However, these methods require more computational resources and may not be necessary for studying CO2 in most cases.

In summary, while simulating CO2 as a flexible molecule using bond constraints may be challenging, it is not impossible and there are alternative methods that can be used. I hope this helps to clarify the issue for you. Best of luck with your simulations!