[lammps-users] Regarding minimization

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1

Hello !

I am a Ph.D student currently studying the unfolding and aggregation pathways of a protein using Molecular Dynamics simulations. I wanted to seek opinion regarding whether it is justified to minimize a system consisting of a folded domain and an unfolded motif. I am concerned mostly about the energetics, whether a system having a folded entity (stable - minimum energy) can be minimized along with an unfolded entity (unstable - maximum energy)?
Kindly suggest it to me.

Regards
Deepshikha Ghosh

2

This is not a question about LAMMPS, but about details of your research. I suggest you discuss this with your adviser or experts in the specific field of research.
I would also like to point out that your notion of minimization and folded/unfolded is extremely simplified and not quite applicable.