From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Mon Apr 13 2020 - 12:24:18 CDT
Thank you for your reply.
To clarify, I am not yet done with step 1, it is continuing it. That is why I am not sure if system is done minimising or not and, consequently, should I keep minimise command when using restart files of first equilibration step and resuming this first equilibration step?
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From: Josh Vermaas <yoshi121212_at_gmail.com> on behalf of Josh Vermaas <joshua.vermaas_at_gmail.com>
Sent: Monday, April 13, 2020 1:16:35 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca>
Subject: Re: namd-l: minimise in restarting first equilibration step
Not unless you want to minimize something after dynamics has started (unlikely). The minimize command should only be active when you want to do minimization, which is usually only the very first equilibration step.
On 4/13/20 8:37 AM, Khoualdi Asma Feriel wrote:
since the first equilibration step was stopped on hitting wall time without finishing, I want to use restart files to resume it. Since it is the first step, should I keep the minimize option in namd configuration file?
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