[gmx-users] Three-site model for acetonitrile

[David]

On Mon, 2003-02-24 at 16:31, Christoph Freudenberger wrote:
> Christoph Freudenberger wrote:
> The simulation is running now, and i looks like it really makes some
> difference... But I have to wait for the longterm behaviour of the
> system to be sure.
> 
> Just to get this thing complete:
> What would be a good guess for the bond and angle force constants?
> For now my acetonitrile.itp looks like this:
> [ bonds ]
> ;  ai  aj funct           c0           c1
> 1       2       1          0.14600     334720. ;C-C
> 2       3       1          0.11600     502080. ;C#N
> 
> [ angles ]
> ;  ai    aj    ak       funct   c0      c1
>      1     2     3       1       180.0  418.400 ;C-C#N
> 
> The values were guessed by using the prodrg server. (BTW: Does anyone know
> why the force constants for bonds given by prodrg are always factor 10
> larger than the corresponding values in ffgmxbon.itp? Anyway, the values
> I chose are consistent with ffgmxbon.itp.)

This is why I was aking about how you keep it linear. The angle will not
work, or will be rather instable at best, since the potential is not
continuous at 180 (i.e. angle <= 180 always). You probably want to
define the C as a dummy particle. Note that you will have to
redistribute the mass over N and CH3 such that centre of mass is
unchanged and inertia tensor is not modified too much either.

(If you do it you'll be able to use much longer timesteps as well)
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular 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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