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
weirdness.
Thanks!
Alex
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