From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Apr 13 2020 - 12:42:24 CDT
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
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------------------------------------------------
> *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
>
>
> 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
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