Jack Shultz wrote:
Hello,
I am fairly new to GROMACS but I have spent time running tutorials for
several other molecular dynamics applications. I would like to know if
the current framework for GROMACS has support for methods that calculate
saddle point energy in first-order reactions. If so, are there examples
I can read about?
First, GROMACS does not support reactions, unless you use the QM/MM
methods in which case you have to look into e.g. Gaussian's way of doing
a Transition State optimization.
Second, you can do normal mode analysis which would give you indirectly
the needed information, if you have a conformation that you know is the
transition state.
Jack
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