From: Neena Susan Eappen (neena.susaneappen_at_mail.utoronto.ca)
Date: Fri Aug 16 2019 - 11:42:32 CDT

Thank you Ashar and Joao,

To use the clustering tool in VMD, I just download the plugin from this site? https://github.com/luisico/clustering/blob/master/clustering.tcl

Thank you,
Neena
________________________________
From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Friday, August 16, 2019 1:11 PM
To: Neena Susan Eappen <neena.susaneappen_at_mail.utoronto.ca>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Extract Most Frequently found structure

Dear Neena,

As long as these 50 (I am assuming) independent simulations are the same in terms of composition (number and sequence of atoms), you can load then into the same molecule. If for some reason they are different, you need to load them into separate molecules.

Regarding the “number of unique structures/ conformations”, you first need to define what is a unique structure/conformation. RMSD would probably be the first choice, but this calculation can mask a lot of different conformations due to its overall system average. Other measurements are more sensitive to local variations like RMSF per residue, the radius of gyration, contact maps. Depending on the system, you can also define distances and angles between domains as a criterion to distinguish conformations. Once you found the right set of measurements, there are several clustering analysis that you can use.

All of these measurements are possible in VMD, requiring more or less scripting on your end, but first, you need to understand your system.

I hope this helps.

Best,

Joćo

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Neena Susan Eappen <neena.susaneappen_at_mail.utoronto.ca>
Date: Thursday, August 15, 2019 at 10:31 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Extract Most Frequently found structure

Hello VMD users,

I simulated a protein 50 times, is there a way to upload all 50 on VMD and figure out number of unique structures/ conformations? In addition, how to figure out the most frequently found structure?

Many thanks,

Neena