[gmx-users] Constraining N-H and H-H bonds in ammonium via SETTLE?
lindahl at cbr.su.se
Wed May 23 21:28:01 CEST 2007
On May 23, 2007, at 9:09 PM, John D. Chodera wrote:
> Hi all,
> Can the SETTLE implementation in gromacs be used to constrain N-H
> and H-H bond lengths in ammonium (NH4+) molecules?
> We have prepared an .itp file (attached below) -- based on the
> Pande group ffamber port -- for ammonium (NH4+). If gromacs could
> settle N-H bonds too, would this involve simply adding the
> following line?
> [ settles ]
> ; OW funct doh dhh
> 1 1 0.101 0.166
No, it won't fly that way. The reason Settle works (and is special)
is that the three atoms form an isolated molecule, so knowing the
forces on all three sites we can solve for the resulting rigid-body
rotation analytically. You can't just add another bond to that
molecule that is constrained the normal way, although in theory you
could create a 5-body SETTLE (probably too expensive).
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