I probably get very confused because I learned to do this with the now obsolete ReadFreeze keyword now it sometimes may seem to me like I’m using double negatives or something – please do not optimize all atoms except if they are hydrogen atoms. The way I selectively optimize hydrogen atoms is by erasing all atoms from the list -using the noatoms instruction- and then selecting which are to be included in the list -with atoms=H-, but I haven’t tried it with only selecting hydrogen atoms from the start, as in atoms=H noatoms atoms=H This list adds, and therefore optimizes, all carbon, hydrogen and sulfur atoms, except atoms 5, 6, 7 and 8, should they be any of the previous elements in the C H S list. If you wish to selectively add some atoms to the list while excluding others, here’s an example: atoms=C H S notatoms=5-8 So, for example you want to optimize all atoms EXCEPT hydrogens, then your input should bear the ReadOptimize keyword in the route section and then, at the end of the molecule specification, the following line: atoms notatoms=H This list is invoked by the ReadOptimize keyword in the route section and it includes all atoms by default, you can then further tell G09 which atoms are to be included or excluded from the optimization. I usually optimize hydrogen atoms when working with crystallographic files but that for some reason I want to preserve the rest of the molecule as refined, in order to keep it under a crystalline field of sorts.Īsking Gaussian to optimize some of the atoms in your molecule requires you to make a list albeit the logic behind it is not quite straightforward to me.
Sometimes you just need to optimize some fragment or moiety of your molecule for a number of reasons -whether because of its size, your current interest, or to skew the progress of a previous optimization- or maybe you want just some kind of atoms to have their positions optimized. A sincere apology to all subscribers for getting a notification to this post when it wasn’t still finished.
#Gaussian software relaxed potential energy scan how to
I still don’t know how to work around this or but will be happy to report it whenever I do. So, if you want a WFN(X) file for post processing an MP2 (or any other post-HartreFock calculation for that matter) ask for it from the beginning of your calculation in the same job. We tried to generate the wfn(x) file with the following keywords at the route section #p guess=(read,only) density=currentīut we kept retrieving the HF values, which we noticed by running the corresponding HF calculation and noticing that every value extracted from the WFN file was exactly the same. We later found out that using a chk file to generate a wfn(x) file using the guess=(read,only) keyword didn’t retrieve the MP2 wavefunction but rather the HF wavefunction! Luckily we realized this problem very quickly and were able to fix it.
A few weeks back we wrote about using WFN(X) files with MultiWFN in order to find σ-holes in halogen atoms by calculating the maximum potential on a given surface.
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