[gmx-users] Re: molecule order optimization?
mrshirts at stanford.edu
Tue Feb 25 14:19:42 CET 2003
The changes in the order did indeed speed up the simulation, by about 30%.
One problem, though is that it is impossible to use settle with this ordering.
If you specify the oxygen in [settles], as so:
[ settles ]
; i funct doh dhh
4 1 0.09572 0.15139
you get the error:
Fatal error: [ file "/home/mrshirts/gmx/share/top/tip4pgmx.itp", line 23 ]:
Atom index (4) in settles out of bounds (1-4)
Settle works on atoms 4, 5 and 6
Presumably, if the contraints are tight enough, then you'll get the same
answer whatever contraint method is used, but it might be useful for settle to
handle other molecular orders.
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