Right, it could be interesting to see a fragment of the simulation after
your treatment using these commands, e.g. to understand the lipid behaviour
(not a protein) on the borders of the box..
Il giorno ven 8 nov 2024 alle ore 10:17 Téletchéa Stéphane <
stephane.teletchea.univ-nantes.fr> ha scritto:
> Le 08/11/2024 à 10:08, Enrico Martinez a écrit :
> > .Stéphane - would it be possible to share a short video of your md
> > system in order that we may understand how the lipids behave on the
> > border of the box ??
> Before or after the treatment ?
>
> I thought the videos where on the preprint server, but not yet it seems.
>
> After the treatment there is no visual artifact.
> Concerning calculations, this has or not effects, depending on what you
> measure.
> For most distances this is not a problem (intra protein distances for
> instances), but
> if you want to do some residence time analysis, you observe large jumps
> in values.
>
> Getting a well imaged system is of utmost importance, and more difficult
> than before,
> with microsecond scale simulations being routine.
>
> Stéphane
>
> --
> Maître de conférences Hors Classe, PEDR, HDR
> US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics,
> F-44000 Nantes
> http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
>
>
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Received on Fri Nov 08 2024 - 01:30:02 PST
