[gmx-developers] Perturbing Proteins

[Mark Abraham]

Hi,

These are good questions for the gmx-users mailing list. On this list we
discuss issues pertaining to the code, rather than the use of the code.
Thanks!

Mark

On Tue, Apr 3, 2018 at 10:26 PM Sanyam Kapoor <sanyam at nyu.edu> wrote:

> 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
> --
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