On Tue, Sep 19, 2023, Zafar,Muhammad Saqlain via AMBER wrote:
>
>I want to get inherent structure after doing my NPT, on trajactory npt.nc
>file.
>
>i want to know is steepest descent method is ok to get inherent structure
>or anyother algorithm i have to use for it ?
You would want to use the "xmin" minimizer, ntmin=3 in sander. See the
Reference Manual for details. If you have explicit solvent, you would want
to remove that first, since minimizing the solvent doesn't make good
physical sense (not to mention being very difficult to converge.)
You should be able to get solvent energies minimized to a very low gradient
(say 10^-7 or even less if you are patient.) This will give you the
inherent structure and its energy. [You may need to turn of SHAKE for this
minimization...I can't quite remember whether sander treats SHAKE correctly
with ntmin=3 -- do some experiments on small systems first.]
....good luck....dac
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Received on Wed Sep 20 2023 - 10:00:03 PDT
