[gmx-users] Lowest energy structure after production MD run

[Neena Susan Eappen]

Hello Simone,

Thank you for detailed reply, I am sorry, I got this incorrect information from my search on google. So the final structure is the state at the final time of simulation or basically the last frame, great!
I am new to gromacs, my goal is to understand the structure of a peptide in vacuum. From my experiments on the millisecond timescale, I see atleast two conformations in vacuum (with distinct collisional cross sections). Yes, that's exactly what I was looking for an energy landscape of my trajectory, to look for atleast two highly populated low energy structures and somehow extract out CCS for those. So far I have tried only 1ns MD run, I am trying to get familiar with all mdp files before I do a 1µs run.
What did you mean by collective variables?

Thank you for sharing your knowledge,
Neena

________________________________
From: Neena Susan Eappen
Sent: Friday, April 5, 2019 3:52 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Lowest energy structure after production MD run

Thank you Dr. Dallas,

I am new to gromacs, so I assumed the final structure was average after searching on google.

Neena




________________________________
From: Neena Susan Eappen
Sent: Friday, April 5, 2019 2:22 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Lowest energy structure after production MD run

Hello gromacs users,

Since the final structure obtained after production MD run is the average structure, how to extract out the lowest energy structure?

Thank you for sharing your knowledge,
Neena