You might also need to adept the whole matrix so the benzene has the right orientation in relation to the NT, so at least three atoms in there need to be somehow defined by atoms in the NT. Oh and of course if you got a more complex system than one atom you want to not only define the distance of that dummy atom but also the angles, so it's in the right position. You can substitute the "Na" line with your cartesian coordinates, but then the numbering in the z-matrix section changes! you have to adopt those numbers. The format basically needs to be exact like this. So here's the input for this, for a first try just from 2.5 in 5 0.5 A steps which at least runs without any errors: # opt=z-matrix hf/3-21g Also the extra lines between the sections are a problem. Trying to fix such a complex system is always very difficult so what I did was using a similar system, I got one sodium atom instead of your NT and I'm moving the benzene away.įirst of all: you got two different dummy atoms in there, atom 1 and atom 9, which I guess makes some problems. If someone can link me to relevant literature regarding (reaction coordinate calculations?) I'm more than willing to look into it as for now this is the method my professor suggested. Is there an issue with my variables and constants section? I've looked at many sample calculations but I didn't find any that consider moving one molecule toward another. I suspect this is a syntax issue since the documentation for "z-matrix" and "scan" suggests it is possible to keep the nanotube coordinates frozen and just scan the benzene molecule.Is there an issue with the route section? I tried replacing "scan" with "opt=modredundant" but that introduces its own errors and its clear I don't know what I'm doing.Scan using 1 unit nanotube with benzene at 2.5 A Here is a my current input file %mem=40GB I've read the Gaussian documentation and it seems like mixing Cartesian and z-matrix coordinates in a scan function is possible but I've tried many different inputs and I still get a "No variables in Z-matrix error." I'm trying to scan from 2.5 to 5.5 angstroms in 0.1 A intervals. I have the optimized Cartesian coordinates for a nanotube and z-matrix for benzene I would like to set up the calculation to calculate the potential energy of the system when the benzene molecule is a distance R away from the NT along the z-axis. I asked a similar question earlier this year but I'm still stuck with a similar problem.īasically I'm trying to implement a scan calculation using both a z-matrix and Cartesian coordinates.
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