On Wed, Dec 18, 2024, Kankana Bhattacharjee via AMBER wrote:
>
>I would like to simulate pyrrole-water system using QM-MM-MD setup.
>Suppose, I have pyrrole-water coordinate/pdb file. So, how can I proceed
>building up the QM-MM-MD setup using amber ?
>Your suggestions would be highly appreciated.
In Amber, you first create an MM-only description of the system. This is
needed to establish charges and Lennard-Jones parameters for all atoms, and
is generally used for an initial equilibration. Then you modify your mdin
file to specify which atoms should be treated as QM, and at what level. This
is all laid out in some detail in Chapter 10 ("QM/MM Calculations") in the
Amber24 Reference Manual.
I would recommend choosing a fast semiempirical method for your initial
QM/MM runs. Study the outputs carefully, to make sure you are getting the
behavor you want. Then you can switch to another quantum model, depending on
what you are trying to learn.
...good luck...dac
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Received on Thu Dec 19 2024 - 08:30:02 PST
