[gmx-users] settle for other solvents
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 18 12:30:48 CET 2003
On Tue, 2003-02-18 at 09:03, Erik Lindahl wrote:
> On Tuesday, Feb 18, 2003, at 02:58 US/Pacific, David van der Spoel
> > On Tue, 2003-02-18 at 08:41, Christoph Freudenberger wrote:
> >> Hi there,
> >> Is it possible to use the settle procedure for other solvents than
> >> spc?
> >> CH2Cl2 should be possible (with a united CH2-group) because it has the
> >> symmetry like the water molecule.
> >> But what about linear molecules like Acetonitrile: Me-C=N?
> >> Or 4-atom models like DMSO?
> >> Me
> >> /
> >> O=S
> >> \
> >> Me
> >> Best regards?
> > Yes, check the topologies for e.g. TIP4P. If you define the Oxygen as a
> > dummy in DMSO it should work. Linear molecules won't work.
> Just a clarification since I just said it wasn't possible:
> Massless dummies are definitely useful for this stuff, but this means
> you are simulating a slightly different molecule; you will not get
> (exactly) the same result as with the normal system with the additional
> constrained bond condition. But it's worth testing!
Ah, I didn't think of that. However, in this particular case it may be
possible to redistribute the masses such that your molecule still has
the same moments of inertia... Maybe not...
OK, got it!
You define the settle plane to be O-Me-Me and have the S as a dummy.
Then you reshuffle the mass of the S over the three atoms until the
moment of inertia is the same... Slightly easier, but still not
one-to-one mapping I'm afraid...
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
More information about the gromacs.org_gmx-users