[gmx-users] Re: molecule order optimization?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 25 18:51:21 CET 2003
On Tue, 2003-02-25 at 14:19, Michael Shirts wrote:
> 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.
this is on the wish list for me too...
just specifying all three atoms should do...
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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