[gmx-users] David, adding new atom types to gromacs "shell model"
spoel at xray.bmc.uu.se
Mon Mar 14 21:45:16 CET 2005
On Tue, 2005-03-15 at 04:19 +0800, xieyh at hkusua.hku.hk wrote:
> Dear David:
> On Tue, 2005-03-15 at 03:09 +0800, xieyh at hkusua.hku.hk wrote:
> >> 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
> I still have polarization? In shell model, the polarization is obtained from the
> definition of [water_polarization] item in sw.itp. However, where is the
> polarization from in the case of giving a mass to shell particle? (can I delete
> the [water_polarization] item in this case?)
No. If you delete the polarization the particle will be not connected.
> I am not very sure. Is that realized by the changes of bond length between shell
> particle and its connected atom (e.g. oxygen in water molecule)?
Please check the itp file together with the manual (ch. 5), and the
> Thanks again.
> Xie YH
> Hong Kong Univ.
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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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