[gmx-users] David, adding new atom types to gromacs "shell model"
spoel at xray.bmc.uu.se
Mon Mar 14 20:29:16 CET 2005
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.
> 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
> Thanks your kind help for so long a time.
> 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
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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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