From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Mon Apr 13 2020 - 13:50:03 CDT
Dear all,
Thank you for both of your kind replies.
>From what I understood, I can continue equilibration first step with a configuration file that specifies 1) restart files, 2) new firsttimestep value, 3) uses run value that is equal to total steps- firsttimesteps and 4) that doesn't specifiy "minimise 1000" as was there in the configuration that was used to start the step in the very beginning.
This was my problem - to know if I need to keep this command since I am still resuming the "first" equilibration step.
Giacomo, thank you, I benefitted from your answer, which points me to know how to judge the if my system was minimized or not.
Best,
Asma Feriel
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: April 13, 2020 1:54 PM
To: NAMD list <namd-l_at_ks.uiuc.edu>; Josh Vermaas <joshua.vermaas_at_gmail.com>
Cc: Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca>
Subject: Re: namd-l: minimise in restarting first equilibration step
Hello Asma, adding to what Josh already described: NAMD will keep running regardless of whether minimization criteria have been fulfilled or not. You should be aware of this because a minimization criterion is actually not given by you (did you give one?), and there is no default one:
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node34.html
Other MD codes have a built-in decision, which stops the run and prints a message if the minimization has been "completed". NAMD by design lets you decide when you have reached a local minimum: all energy terms are printed with several digits of precision in the standard output.
Was this the problem? If not, it'd be hard to tell given the few details.
Giacomo
On Mon, Apr 13, 2020 at 1:43 PM Josh Vermaas <joshua.vermaas_at_gmail.com<mailto:joshua.vermaas_at_gmail.com>> wrote:
Hi Asma,
Maybe I wasn't clear enough the first time, but you only put minimize in the configuration file when you want to minimize. If you've already started doing dynamics after minimizing in the first part of equilibration, you wouldn't want to start minimizing again, would you? I would take it out if the minimization steps have already completed.
-Josh
On 4/13/20 11:24 AM, Khoualdi Asma Feriel wrote:
Hello,
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?
Thank you.
Asma Feriel
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________________________________
From: Josh Vermaas <yoshi121212_at_gmail.com><mailto:yoshi121212_at_gmail.com> on behalf of Josh Vermaas <joshua.vermaas_at_gmail.com><mailto:joshua.vermaas_at_gmail.com>
Sent: Monday, April 13, 2020 1:16:35 PM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu><mailto:namd-l_at_ks.uiuc.edu>; Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca><mailto:asma.feriel.khoualdi_at_umontreal.ca>
Subject: Re: namd-l: minimise in restarting first equilibration step
Hi Asma,
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.
-Josh
On 4/13/20 8:37 AM, Khoualdi Asma Feriel wrote:
Hello,
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?
Best,
Asma Feriel
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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