From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Dec 14 2020 - 09:42:23 CST
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----- On 14 Déc 20, at 5:20, Ropón-Palacios biodano.geo_at_gmail.com wrote:
> Dear Prof. Jérôme,
> I’m using colvar for pulling water this is best but and have any question;
> 1. How can i make to that water not cross PCB box ?
Generally you cannot, and there is no good reason to do it. By default collective variables in the Colvars Module are caculated using the periodic conditions, so it doesn't really matter whether a molecule crosses the boundary or not, and it doesn't matter whether or not the coordinates are wrapped (if the atom group is a single water molecule).
> 2. Why when use same protocol for pulling any times, time necessary for pulling
> is 15 mil steps other times is 5 mil steps?
That depends on the specific biasing algorithm you are using. You didn't say what it is.
> 3. When pulling 8 to -30 reacction coordínate pulling is to +Z, but si change 8
> to -8 pulling is rigth? , for get center in Z of water i’m using “measure
> center” into VMD.
Sorry I'm not sure what the question is.
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