From: Hélder Bandarra Tavares (
Date: Mon Jun 01 2020 - 11:24:27 CDT

Dear Daniel,

First of all, thanks for your help.

I'm trying to calculate the distance between two proteins that are bound by a linker molecule. Since it would be too time-consuming to simulate the whole system, I decided to run a simulation of the linker alone in solution. Worth noting that I only need an estimate of this value, just to have an idea of the distance. So I don't need super accurate results.

What is Dynamics data? I think that having a Boltzmann distribution of the linker's length would be perfect.

Thank you for the suggestions, I will look into it.

Kind regards,
Hélder Tavares
From: Daniel Fellner <>
Sent: 01 June 2020 18:14:29
To: Hélder Bandarra Tavares
Subject: Re: vmd-l: How to determine a molecule's conformation in solution

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 <<>> 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