- Gaussian software relaxed potential energy scan is this dft how to#
- Gaussian software relaxed potential energy scan is this dft full#
- Gaussian software relaxed potential energy scan is this dft trial#
More often than not it is trial and error. There are traps and pitfalls lining your way. You can see, that with these small molecules it is already hard to predict what happens when you run the calculation. Theoretically this should give us 20 data points. We will scan also both of the oxygen oxygen distances. Just for shits and giggles, let's do one that will make us cringe. not everything will run smoothly and sometimes the calculation turns rogue and fails. For the given set of parameters, this is the lowest energy. There is a sudden rotation at 2.8 angstrom. With the result, we'll see again something unexpected happening.
If you are interested in keeping at least the bond angles constant, freeze them: Only one coordinate is fixed, which is the distance between the carbons. This is expected behaviour in a relaxed scan. The CO bond lengths changes, too, but that is not as visible. You can see that the OCO bond angles changes. That will give us the following graph and animation: I chose five steps with an increment of -0.2 angstrom. We can simply scan over the "bond length" of the carbon carbon distance. First we need to transform the coordinates in a way that we can understand which molecule to move where. If we would use the approach you have come up with, this would be really tedious. Now we want to move the two molecules closer together. The result will be the following geometry: In you case you specify 12 coordinates to scan with 20 points each, resulting in a whopping $N=\frac$ and I am using the ridiculous low level of theory HF/3-21G.įirst up optimise the equilibrium geometry. This allows you to systematically, brute force a potential energy surface.
Gaussian software relaxed potential energy scan is this dft full#
you will step one variable, fix the values of the scanned coordinates, and run a full optimisation at this point. Using this interface you will perform a relaxed scan, i.e. Constructing a meaningful modredundant calculation is quite a difficult task, as you sometimes cannot anticipate what the program actually does. Thanks is (probably) not going to work the way you intend it to work.
Gaussian software relaxed potential energy scan is this dft how to#
I'll try to look up how to construct the proper z-matrix if that is indeed the best way to do things. I guess my question is now if this is a plausible approach. Specifically I want to keep all bond angles the same but move atoms 101-112 in 0.2 A steps in the z direction, and calculate the potential energy. The thing is, I'm not sure quite how to edit the z-matrix (relevant part below) with the scan commands. That's what I initially came across but with ~100 atoms, I just let Chemcraft generate the z matrix from my cartesian coordinates. And putting your brain to that task is also a bit tedious. The only downside to this approach is, that you need a z-matrix to make it work. Oftentimes a nice little rigid scan will give you a decent result. Thankfully a full relaxed scan is not necessary in most cases. I decided to try smaller increments to increase the resolution but I have quite a few more situations to test so I wanted to just have Gaussian change the increments and recalculate the potential energy. Before, I just ran the "#P BP86/6-311++G**"" with my arene 3.0 angstrom apart and made new input files changing the arene z coordinates in 0.5 angstrom increments but I can't capture that potential energy well. I'm trying to find the distance apart where the two molecules are stabilized. One is a nanotube and the other is an arene and my task was to basically generate this plot. I have already optimized my two molecules.
Do I have to change any other commands? The only parameters set are the resource limits and "#P BP86/6-311++G**" Here is what I haveįrom my understanding, this should just move up all of the atoms of the top molecule by 0.2 angstroms in the Z direction.ĭo I just throw this stuff anywhere into the input file? What about the original cartesian coordinate array? Surely it has to stay since the "step" array calls back to atoms 101-112. I tried following this site's advice īut I'm not sure I constructed the input file correctly. I have the basis set/ correlation methods I need to use and the cartesian coordinates for all the atoms when they are arranged 3.0 angstroms apart. My professor told me gaussian has a scan function to do this but I'm having trouble figuring some things out. I have the cartesian coordinates for two molecules that are in a stacked position and I want to be able to calculate the potential energy at 0.2 angstrom steps from when the top molecule is 3.0 angstroms to 7.0 angstroms away in the z direction.
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