VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Mon Jun 01 2020 - 21:04:57 CDT

I see, in that case you would probably want to grab the length of the
molecule in each frame of the simulation. You could then bin the values to
create a histogram, this would show you the Boltzmann distribution of the
length.

You could accomplish this with a tcl script using the vmd 'bond' command:
https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html

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

On Tue, 2 Jun 2020 at 04:24, Hélder Bandarra Tavares <
H.D.BandarraTavares_at_tudelft.nl> wrote:

> 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 <dfel694_at_aucklanduni.ac.nz>
> *Sent:* 01 June 2020 18:14:29
> *To:* Hélder Bandarra Tavares
> *Cc:* vmd-l_at_ks.uiuc.edu
> *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 <
> 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
>>
>