[gmx-users] Perturbing Proteins

[Sanyam Kapoor]

Hi all,

I was wondering if there is a principled way to perturb molecules and then
see its energy converge to the stationary state via the simulation.
Perturbation could mean changing the coordinates of the atoms, changing
angles dihedrals etc. Anything related to the topology. I want to see this
without the addition of any solvents in the environment.

My concern is that if I perturb randomly, the molecule may no more remain
in a valid state (bad bond distance or bad angles/dihedrals etc.). Any
ideas here?

Another question is that if I pick up any molecule from Protein DataBank
and run a simulation without any solvent addition, does it converge further
or are those molecules already on some minimum energy value attainable?

Please correct me if I miss some part of the molecular dynamics pipeline.
-- 
Regards,
Sanyam Kapoor
Masters in Computer Science
Courant Institute, New York University
https://www.sanyamkapoor.com