VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Mon Jun 01 2020 - 11:14:29 CDT

Molecules are dynamic by nature, so the question is akin to asking how long
is a piece of string?

Dynamics data gives you a Boltzmann distribution of the system under
specific conditions, it might be helpful to know what you are hoping to use
the data for.

Another potential issue is sampling: If you're in a deep local minimum, a
nonbiased simulation may take a long time to reach the global minimum. You
could consider trying a simulated annealing protocol or well-tempered
metadynamics.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Tue, 2 Jun 2020 at 04:05, Hélder Bandarra Tavares <
H.D.BandarraTavares_at_tudelft.nl> wrote:

> I want to determine the length of a molecule in 0.3 M KCl and I was
> wondering if it would be feasible with NAMD. I minimized/equilibrated it
> after solvation under the right conditions but the resulting conformation
> is very similar to the initial one, with almost the same length, so I'm not
> sure what to conclude from that.
>
>
> I also ran a production simulation and got multiple conformations, but I'm
> not sure what to conclude from that either. Would the production frame with
> the lowest energy give me the right conformation and length?
>
>
> I appreciate any help/thoughts on this.
>
>
> Hélder Tavares
>