jmichel80
commented
6 years ago Hi @carajillu there may well be a problem that I missed in my tests. Perhaps the issue becomes apparent when a molecule drifts out of the minimum image.
Better to assign the issue to yourself, you are more familiar than me with the code by now and I doubt i can go deep in the code before a while.
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On 20 Jul 2018, at 15:58, carajillu notifications@github.com<mailto:notifications@github.com> wrote:
I think there is a problem between the way atoms are read and the makeWhole() call just before updating the grid. The plumed developers manual says that makeWhole() makes atoms whole (which I am not sure what it means) "assuming they are in the proper order", but the vector that contains the atom numbers to request is built first with the polar apolar atoms, then with the polar atoms (lines 457-467), which means that they are not in order, so that might be altering the way the atoms are "made whole" and that could be affecting the score. Mentioned lines are in the devel branch
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carajillu
I think there is a problem between the way atoms are read and the makeWhole() call just before updating the grid. The plumed developers manual says that makeWhole() makes atoms whole (which I am not sure what it means) "assuming they are in the proper order", but the vector that contains the atom numbers to request is built first with the polar apolar atoms, then with the polar atoms (lines 457-467), which means that they are not in order, so that might be altering the way the atoms are "made whole" and that could be affecting the score. Mentioned lines are in the devel branch