[gmx-users] David, adding new atom types to gromacs "shell model"

[David]

On Tue, 2005-03-15 at 03:09 +0800, xieyh at hkusua.hku.hk wrote:
> Dear David:
> 
> The following is one email you replied previously. 
> 
> I am a little confused with "give shell a mass and do normal dynamics". 
> 
> Let me guess, normally, in shell model, the shell particle is massless and
> [water_polarization] item should be considered in sw.itp. However, if using
> approximating method, we can appoint a small mass to shell particle. What I
> wanna know is about the meaning of normal dynamics. 
If you give it a mass you can in principle treat it as a normal particle
(you'll have to change the particle type to A from S).

However you need to take very short time steps for this to work (e.g.
0.1 fs).

> 
> In detail, if a mass is given to shell, then we need not consider
> [water_polarization] any more? Is it right? On the contrary, I just need to
> define [bond], [angle] etc items for describing the connection of shell
> particle to dummies or other atoms? Could you help me to confirm myself?
> 
Yes you still have polarization but you do not optimize the shell
position at each time step. This is the way e.g. DL_POLY treats shell
particles.


> Thanks your kind help for so long a time.
> 
> 
> Regards,
> 
> Xie YH
> Hong Kong Univ.
> 
> 
> 
> 
> On Wed, 2004-05-05 at 02:36, Julius Su wrote:
> > >Hello,
> > >
> > >I had some questions about the shell model implemention in GROMACS --
> > >
> > >(1) is it possible to define new shell types?
> >Can you make yourself more clear? Right now a shell is a point charge
> >connected to another particle (or dummy position) with a spring. The
> >shell is massless and its position is optimised at every time step.
> >Obviously one can also give them a mass (e.g. 1 amu) and do normal
> >dynamics.
> ...
> ...
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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