VMD-L Mailing List

From: Hélder Bandarra Tavares (H.D.BandarraTavares_at_tudelft.nl)
Date: Tue Jun 02 2020 - 04:39:16 CDT

Thank you very much! I think that with this information I'll be able to get an estimate of the length.

Just to be sure: by simulation you mean the production run? Since in my case my equilibration run yielded basically the initial structure over every frame, which would probably affect my conclusions if I took it into account.

Kind regards,

Helder Tavares

________________________________
From: Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
Sent: 02 June 2020 04:04:57
To: Hélder Bandarra Tavares
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: How to determine a molecule's conformation in solution

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--_000_57575cc162dd44dcbf3f18705fbf6b72tudelftnl_--