nebmake.pl didn't give the ideal pathway that I want

lanjh · Post by **lanjh** » Sun Apr 08, 2007 1:13 am

hi, sir!
I want to do a neb calculation. But when I generate the reaction pathway with nebmake.pl, it didn't generate the reasonable one! I want to know how to solve this problem~~~

thanks

Post by **graeme** » Sun Apr 08, 2007 1:56 am

This is not enough information to know what is wrong with your initial path. The nebmake.pl script generates a linear pathway between your specified endpoints.

If the problem is related to two (or more) atoms getting close together in the linear path, you can try using the nebavoid.pl script to push them apart. This has been discussed before:

viewtopic.php?t=172

lanjh · Post by **lanjh** » Sun Apr 08, 2007 2:27 am

thank you for your reply, sir! it involves the reaction
NH + 2O--NO + OH
and the two oxygen atoms locate at the opposite two sides. Using nebmake.pl, in one of the intermediates, the two O redistribute to one side. the O and H superpose.
what about this question>

Post by **graeme** » Sun Apr 08, 2007 2:50 am

If you want to find a path that is qualitatively different from the linear path, you need to manually construct a different initial path. You're pretty much on your own here because we do not have automatic ways of sampling different paths. One possibility is to use different initial and final states. If these molecules are in the gas phase, you could choose different orientations of the molecules that result in a pathway closer to the one you are thinking of. Perhaps even better is to use an intermediate structure. If you construct a configuration similar to the transition state you have in mind, you can then form an NEB from two pathways - one from the initial state to the intermediate, and the second from the intermediate to the final state. Good luck.

lanjh · Post by **lanjh** » Sun Apr 08, 2007 3:10 am

thanks for your reply!