[gmx-users] Lost particles while sorting

Alex nedomacho at gmail.com
Fri Nov 3 02:33:14 CET 2017

On 11/2/2017 7:18 PM, Mark Abraham wrote:
> Granted. There's a bajillion ways for a newcomer to any simulation type to
> shoot themselves in the foot. Where would be a good place for "with walls,
> set up your simulation cell so the initial positions of all the particles
> are on the correct side of the wall?"
See, because I am very far from a newcomer here, it became almost 
immediately after I posted initially. But we do have many newcomers who 
appear to have treated walls as a bug to the point of taking it to 
redmine. Even your first reaction was to take it there. I see your point 
very well, and it's both true and funny (essentially "set up your system 
like you're not an idiot"), but maybe we could say that lost particles 
are often caused by lack of outer vacuum layer between the system and 
the walls prior to running things. Just a suggestion, because everything 
seems to be okay in my simulation. :) Well, except for...
> That combination is one of the very large number of things in GROMACS that
> I know very little about. But a new topic might get the interest of any who
> do know!
... for this combination. I will post as soon as I can confirm this 



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